Mercurial > repos > nilesh > rseqc

annotate geneBody_coverage.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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60
1421603cc95b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
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1 <tool id="rseqc_geneBody_coverage" name="Gene Body Coverage (BAM)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
1421603cc95b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
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2 <description>read coverage over gene body</description>
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dbedfc5f5a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 247059e2527b66f1dbecf1e61496daef921040c3"
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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>
dbedfc5f5a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 247059e2527b66f1dbecf1e61496daef921040c3"
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <version_command><![CDATA[geneBody_coverage.py --version]]></version_command>
dbedfc5f5a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 247059e2527b66f1dbecf1e61496daef921040c3"
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10 <command><![CDATA[
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11 #if str($batch_mode.batch_mode_selector) == "merge":
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12 #import re
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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13 #set $input_list = []
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14 #for $i, $input in enumerate($batch_mode.inputs):
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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15 #set $safename = re.sub('[^\w\-_]', '_', $input.element_identifier)
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16 #if $safename in $input_list:
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17 #set $safename = str($safename) + "." + str($i)
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18 #end if
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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19 $input_list.append($safename)
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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20 ln -sf '${input}' '${safename}.bam' &&
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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21 ln -sf '${input.metadata.bam_index}' '${safename}.bam.bai' &&
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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22 echo '${safename}.bam' >> 'input_list.txt' &&
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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23 #end for
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24 geneBody_coverage.py -i 'input_list.txt' -r '${refgene}' --minimum_length ${minimum_length} -o output
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25 #else
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26 #set $safename = re.sub('[^\w\-_]', '_', $batch_mode.input.element_identifier)
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27 ln -sf '${batch_mode.input}' '${safename}.bam' &&
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28 ln -sf '${batch_mode.input.metadata.bam_index}' '${safename}.bam.bai' &&
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29 geneBody_coverage.py -i '${safename}.bam' -r '${refgene}' --minimum_length ${minimum_length} -o output
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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30 #end if
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31 ]]>
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32 </command>
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33
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34 <inputs>
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35 <conditional name="batch_mode">
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36 <param name="batch_mode_selector" type="select" label="Run each sample separately, or combine mutiple samples into one plot">
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37 <option value="batch" selected="true">Run each sample separately</option>
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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38 <option value="merge">Combine multiple samples into a single plot</option>
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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39 </param>
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40 <when value="batch">
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41 <param name="input" type="data" label="Input .bam file" format="bam" help="(--input-file)"/>
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42 </when>
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43 <when value="merge">
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44 <param name="inputs" type="data" label="Input .bam file(s)" format="bam" help="(--input-file)" multiple="true"/>
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45 </when>
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46 </conditional>
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47 <expand macro="refgene_param" />
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48 <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length (default: 100)" help="Minimum mRNA length in bp, mRNA that are shorter than this value will be skipped (--minimum_length)." />
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49 <expand macro="rscript_output_param" />
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50 </inputs>
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51
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52 <outputs>
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53 <data name="outputcurvespdf" format="pdf" from_work_dir="output.geneBodyCoverage.curves.pdf" label="${tool.name} on ${on_string} (Curves pdf)" />
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54 <data name="outputheatmappdf" format="pdf" from_work_dir="output.geneBodyCoverage.heatMap.pdf" label="${tool.name} on ${on_string} (HeatMap pdf)">
52
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55 <filter>batch_mode['batch_mode_selector'] == 'merge' and len(inputs) >= 3</filter>
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56 </data>
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57 <expand macro="rscript_output_data" filename="output.geneBodyCoverage.r" />
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58 <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (text)" />
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59 </outputs>
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60
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61 <!-- PDF Files contain R version, must avoid checking for diff -->
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62 <tests>
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63 <test>
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64 <conditional name="batch_mode">
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65 <param name="batch_mode_selector" value="batch" />
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66 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
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67 </conditional>
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68 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" />
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69 <param name="rscript_output" value="true" />
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70 <output name="outputcurvespdf" file="output.geneBodyCoverage.curves.pdf" compare="sim_size" />
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71 <output name="outputr" file="output.geneBodyCoverage_r" />
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72 <output name="outputtxt" file="output.geneBodyCoverage.txt" />
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73 </test>
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74 <test>
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75 <conditional name="batch_mode">
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76 <param name="batch_mode_selector" value="merge" />
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77 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
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78 </conditional>
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79 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
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80 <param name="rscript_output" value="true" />
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81 <output name="outputcurvespdf" file="output2.geneBodyCoverage.curves.pdf" compare="sim_size" />
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82 <output name="outputheatmappdf" file="output2.geneBodyCoverage.heatMap.pdf" compare="sim_size" />
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83 <output name="outputr" file="output2.geneBodyCoverage_r" />
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84 <output name="outputtxt" file="output2.geneBodyCoverage.txt" />
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85 </test>
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86
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87 </tests>
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88
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89 <help><![CDATA[
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90 ## geneBody_coverage.py
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91
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92 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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93
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94 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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95
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96 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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97 Coverage skewness was measured by `Pearson’s skewness coefficients <http://en.wikipedia.org/wiki/Skewness#Pearson.27s_skewness_coefficients>`_
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98
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99 .. image:: $PATH_TO_IMAGES/geneBody_workflow.png
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100 :width: 800 px
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101 :scale: 80 %
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102
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103
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104 ## Inputs
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105
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106 Input BAM/SAM file
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107 Alignment file in BAM/SAM format.
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108
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109 Reference gene model
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110 Gene Model in BED format.
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111
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112 Minimum mRNA length
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113 Minimum mRNA length (bp). mRNA that are shorter than this value will be skipped (default is 100).
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114
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115 ## Outputs
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116
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117 Text
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118 Table that includes the data used to generate the plots
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119
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120 R Script
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121 R script file that reads the data and generates the plot
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122
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123 PDF
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124 The final plot, in PDF format
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125
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126 Example plots:
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127 .. image:: $PATH_TO_IMAGES/Aug_26.geneBodyCoverage.curves.png
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128 :height: 600 px
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129 :width: 600 px
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130 :scale: 80 %
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131
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132 .. image:: $PATH_TO_IMAGES/Aug_26.geneBodyCoverage.heatMap.png
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133 :height: 600 px
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134 :width: 600 px
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135 :scale: 80 %
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136
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137 @ABOUT@
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138
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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>