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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit 87fad8a906abdb9dc2ecaa2457fb26ab2b09895d
author artbio
date Tue, 11 Jul 2017 13:10:00 -0400
parents 234b83159ea8
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234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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1 <tool id="artbio_size_histogram" name="Generate read size histograms" version="1.0.0">
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2 <description>from alignment files</description>
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3 <requirements>
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4 <requirement type="package" version="1.2.0=py27_0">bowtie</requirement>
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5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
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6 <requirement type="package" version="1.9.3">numpy</requirement>
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7 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
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8 <requirement type="package" version="0.6_28=r3.3.2_0">r-latticeextra</requirement>
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9 <requirement type="package" version="2.2.1=r3.3.2_0">r-gridextra</requirement>
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10 </requirements>
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11 <command detect_errors="exit_code"><![CDATA[
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12 python '$__tool_directory__'/size_histogram.py
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13 #if $refGenomeSource.genomeSource == "history":
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14 --reference_fasta ## sys.argv[2]
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15 '$refGenomeSource.ownFile' ## index source
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16 #else:
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17 #silent reference= filter( lambda x: str( x[0] ) == str( $refGenomeSource.series[0].input.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1]
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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18 --reference_bowtie_index
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19 '$reference'
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20 #end if
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21 --output_size_distribution
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22 '$size_distribution_dataframe'
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23 --minquery
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24 $minquery
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25 --maxquery
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26 $maxquery
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27 --input
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28 #for $i in $refGenomeSource.series
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29 '$i.input'
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30 #end for
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31 --ext
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32 #for $i in $refGenomeSource.series
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33 '$i.input.ext'
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34 #end for
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35 --label
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36 #for $i in $refGenomeSource.series
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37 "$i.input.element_identifier"
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38 #end for
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39 #if $gff:
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40 --gff '$gff'
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41 #end if
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42 #if $global.value == 'yes':
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43 --global_size
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44 #end if
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45 #if $collapsestrands.value == 'yes':
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46 --collapse
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47 #end if
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48 --normalization_factor
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49 #for $i in $refGenomeSource.series
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50 $i.norm
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51 #end for
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52 &&
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53 Rscript '$__tool_directory__'/size_histogram.r
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54 --global '$global'
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55 --size_distribution_tab '$size_distribution_dataframe'
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56 --size_distribution_pdf '$size_PDF'
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57 --title '$title'
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58 --ylabel '$ylabel'
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59 --yrange '$yrange'
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60 --rows_per_page '$rows_per_page'
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61 ]]></command>
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62 <inputs>
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63 <conditional name="refGenomeSource">
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64 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
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65 <option value="indexed">Use a built-in index</option>
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66 <option value="history">Use one from the history</option>
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67 </param>
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68 <when value="indexed">
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69 <repeat name="series" title="Add alignment files">
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70 <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam">
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71 <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/>
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72 </param>
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73 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/>
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74 </repeat>
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75 </when>
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76 <when value="history">
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77 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
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78 <repeat name="series" title="Add alignment files">
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79 <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"/>
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80 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/>
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81 </repeat>
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82 </when>
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83 </conditional>
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84 <param name="gff" type="data" format="gff,gff3" optional="true" label="Optional: select a GFF to investigate regions of interest" help="GFF must match genome build"/>
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85 <!-- <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="GFF database and alignment file databse do not match!"/> -->
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86 <param name="global" type="select" label="Generate size distribution for each item, or generate a global alignment">
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87 <option value="no">for each item</option>
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88 <option value="yes">global</option>
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89 </param>
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90 <param name="collapsestrands" type="select" label="Whether + and - reads should be collapsed or not">
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91 <option value="no">Do not collapse</option>
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92 <option value="yes">Collapse + and - reads</option>
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93 </param>
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94 <param name="minquery" type="integer" size="3" value="18" label="Min size of reads to plot" help="'15' = 15 nucleotides"/>
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95 <param name="maxquery" type="integer" size="3" value="28" label="Max size of reads to plot" help="'30' = 30 nucleotides"/>
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96 <param name="title" type="text" size="15" value="Size distribution" label="Main Titles"/>
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97 <param name="xlabel" type="text" size="15" value="Size in nucleotides" label="x axis label"/>
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98 <param name="ylabel" type="text" size="15" value="Number of reads" label="y axis label"/>
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99 <param name="yrange" type="integer" size="3" value="0" label="y axis range for size distributions. 0 means auto-scaling."/>
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100 <param name="rows_per_page" type="text" size="9" value="8" label="How many items to display per page?">
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101 <validator type="in_range" min="6" max="20" message="Select between 6 and 20 rows, as the readability will suffer otherwise."/>
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102 </param>
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103 </inputs>
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104
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105 <outputs>
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106 <data format="tabular" name="size_distribution_dataframe" label="Size_distribution_dataframe.tab"/>
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107 <data format="pdf" name="size_PDF" label="Size_distribution.pdf"/>
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108 </outputs>
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109
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110 <help>
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111
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112 **What it does**
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113
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114 Takes one or more alignment files (BAM, SAM or tabular bowtie output) as input and produces a histogram of read sizes,
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115 where by default for each "chromosome" a histogram of read sizes is drawn.
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116 Reads that map in sense are on the top (red), reads that map antisense are on the bottom (blue).
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117
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118
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119 .. class:: warningmark
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120
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121 '''TIP''' The input data can be produced using the sRbowtie tool.
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122
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123 ----
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124
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125 '''Example'''
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126
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127 Query sequence::
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128 For a SAM file as the following:
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129
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130 5 16 2L_79 24393 255 17M * 0 0 CCTTCATCTTTTTTTTT IIIIIIIIIIIIIIIII XA:i:0 MD:Z:17 NM:i:0
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131
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132 11 0 2R_1 12675 255 21M * 0 0 AAAAAAAACGCGTCCTTGTGC IIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:21 NM:i:0
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133
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134 2 16 2L_5 669 255 23M * 0 0 TGTTGCTGCATTTCTTTTTTTTT IIIIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:23 NM:i:0
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135
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136 produce a plot like this:
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137
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138 ----
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139
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140 .. image:: static/images/size_histogram.png
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141 :height: 800
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142 :width: 500
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143
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144 </help>
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145 <tests>
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146 <test>
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147 <param name="genomeSource" value="history" />
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148 <param name="ownFile" value="transposons.fasta" ftype="fasta" />
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149 <param name="series_0|input" value="sample1.srbowtie_out" ftype="tabular"/>
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150 <param name="series_0|norm" value="1" />
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151 <param name="series_1|input" value="sample2.srbowtie_out" ftype="tabular"/>
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152 <param name="series_1|norm" value="1" />
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153 <param name="series_2|input" value="sample3.srbowtie_out" ftype="tabular"/>
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154 <param name="series_2|norm" value="1" />
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155 <param name="global" value="no" />
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156 <param name="collapsestrands" value="no" />
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157 <param name="minquery" value="18"/>
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158 <param name="maxquery" value="30"/>
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159 <param name="title" value="Size distribution"/>
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160 <param name="xlabel" value="Size in nucleotides"/>
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161 <param name="ylabel" value="Number of reads"/>
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162 <param name="rows_per_page" value="10"/>
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163 <output name="size_distribution_dataframe" ftype="tabular" file="Size_distribution_dataframe.tab" />
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164 <output name="size_PDF" ftype="pdf" file="Size_distribution.pdf" />
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165 </test>
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166 </tests>
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167 </tool>
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168