Mercurial > repos > nilesh > rseqc

annotate bam2wig.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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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_bam2wig" name="BAM to Wiggle" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
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2 <description>
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3 converts all types of RNA-seq data from .bam to .wig
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4 </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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5 <expand macro="bio_tools"/>
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6 <macros>
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7 <import>rseqc_macros.xml</import>
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8 </macros>
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9
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10 <expand macro="requirements" />
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12 <expand macro="stdio" />
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14 <version_command><![CDATA[bam2wig.py --version]]></version_command>
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15
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16 <command><![CDATA[
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1421603cc95b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
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17 @BAM_SAM_INPUTS@
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18 bam2wig.py -i 'input.${extension}' -s '${chromsize}' -o outfile
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19
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20 #if str($strand_type.strand_specific) == "pair"
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21 -d
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22 #if str($strand_type.pair_type) == "sd"
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23 '1++,1--,2+-,2-+'
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24 #else
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25 '1+-,1-+,2++,2--'
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26 #end if
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27 #end if
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28
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29 #if str($strand_type.strand_specific) == "single"
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30 -d
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31 #if str($strand_type.single_type) == "s"
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32 '++,--'
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33 #else
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34 '+-,-+'
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35 #end if
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36 #end if
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37
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09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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38 #if str($wigsum_type.wigsum_type_selector) == "normalize":
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39 -t ${wigsum_type.totalwig}
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40 #end if
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09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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41
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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42 @MULTIHITS@
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43 ]]>
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44 </command>
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45 <inputs>
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46 <expand macro="bam_param" />
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47 <param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" help="(--chromSize)"/>
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48 <expand macro="multihits_param" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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49 <conditional name="wigsum_type">
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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50 <param name="wigsum_type_selector" type="select" label="Normalization">
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51 <option value="normalize">Normalize to specified sum</option>
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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52 <option value="raw" selected="true">Do not normalize</option>
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53 </param>
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54 <when value="normalize">
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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55 <param name="totalwig" value="" type="integer" label="specified wigsum" help="(--wigsum)"/>
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56 </when>
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57 <when value="raw"/>
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58 </conditional>
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59 <expand macro="strand_type_param" />
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60 </inputs>
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62 <outputs>
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63 <data format="wig" name="output" from_work_dir="outfile.wig">
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64 <filter>strand_type['strand_specific'] == 'none'</filter>
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65 </data>
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66 <data format="wig" name="outputfwd" from_work_dir="outfile.Forward.wig" label="${tool.name} on ${on_string} (Forward Reads)">
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67 <filter>strand_type['strand_specific'] != 'none'</filter>
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68 </data>
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69 <data format="wig" name="outputrv" from_work_dir="outfile.Reverse.wig" label="${tool.name} on ${on_string} (Reverse Reads)">
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70 <filter>strand_type['strand_specific'] != 'none'</filter>
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71 </data>
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72 </outputs>
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74 <tests>
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75 <test>
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76 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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77 <param name="chromsize" value="hg19.chrom.sizes"/>
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78 <output name="output" file="testwig.wig"/>
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79 </test>
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80 <test>
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81 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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82 <param name="chromsize" value="hg19.chrom.sizes"/>
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83 <param name="multihits_type_selector" value="skip_multihits"/>
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84 <param name="mapq" value="20"/>
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85 <output name="output" file="testwig.wig"/>
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86 </test>
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87 <test>
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88 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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89 <param name="chromsize" value="hg19.chrom.sizes"/>
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90 <param name="strand_specific" value="pair"/>
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91 <param name="pair_type" value="sd"/>
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92 <output name="outputfwd" file="testwig.Forward.wig"/>
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93 <output name="outputrv" file="testwig.Reverse.wig"/>
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94 </test>
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95 <test>
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96 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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97 <param name="chromsize" value="hg19.chrom.sizes"/>
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98 <param name="wigsum_type_selector" value="normalize"/>
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99 <param name="totalwig" value="100"/>
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100 <output name="output" file="testwig_wigsum100.wig"/>
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101 </test>
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102 </tests>
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103
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104 <help><![CDATA[
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105 bam2wig.py
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106 ++++++++++
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107
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108 Visualization is the most straightforward and effective way to QC your RNA-seq
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109 data. For example, change of expression or new splicing can be easily checked
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110 by visually comparing two RNA-seq tracks using genome browser such as UCSC_,
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111 IGB_ and IGV_. `bam2wig.py` converts all types of RNA-seq data from BAM_
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112 format into wiggle_ format in one-stop. wiggle_ files can then be easily
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113 converted into bigwig_. Bigwig is indexed, binary format of wiggle file, and
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114 it's particular useful to display large, continuous dataset on genome
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115 browser.
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116
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117 Inputs
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118 ++++++++++++++
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119
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120 Input BAM file
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121 Alignment file in BAM format (SAM is not supported). BAM file will be sorted and indexed using samTools.
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122
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123 Chromosome size file
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124 Tab or space separated text file with 2 columns: first column is chromosome name, second column is size of the chromosome. Chromosome names (such as "chr1") should be consistent between this file and BAM file.
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125
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126 Specified wigsum (default=none)
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127 Specified wigsum. Wigsum of 100000000 equals to coverage achieved by 1 million 100nt reads. Ignore this option to disable normalization.
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128
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129 Skip multiple Hit reads
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130 skips multiple hit reads or only use uniquely mapped reads
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131
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132 Strand-specific (default=none)
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133 How read(s) were stranded during sequencing. If you are not sure about the strand rule, run infer_experiment.py
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134
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135 Outputs
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136 ++++++++++++++
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137
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138 If RNA-seq is not strand specific, one wig file will be generated, if RNA-seq
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139 is strand specific, two wig files corresponding to Forward and Reverse will be generated.
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140
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141 @ABOUT@
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142
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143 .. _UCSC: http://genome.ucsc.edu/index.html
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144 .. _IGB: http://bioviz.org/igb/
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145 .. _IGV: http://software.broadinstitute.org/software/igv/
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146 .. _BAM: http://genome.ucsc.edu/goldenPath/help/bam.html
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147 .. _wiggle: http://genome.ucsc.edu/goldenPath/help/wiggle.html
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148 .. _bigwig: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
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149 ]]>
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150 </help>
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151
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152 <expand macro="citations" />
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153
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154 </tool>