Mercurial > repos > geert-vandeweyer > coverage_report

comparison CoverageReport.xml @ 4:2799221681dd draft

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author geert-vandeweyer
date Thu, 13 Feb 2014 04:45:56 -0500
parents ea32a329aced
children 86df3f847a72
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3:39c374d4cba7 4:2799221681dd
1 <tool id="CoverageReport" name="Panel Coverage Report" version="0.0.2"> 1 <tool id="CoverageReport2" name="Panel Coverage Report" version="0.0.2">
2 <description></description> 2 <description></description>
3
3 <command interpreter="perl"> 4 <command interpreter="perl">
4 CoverageReport.pl 5 CoverageReport.pl
5 ## input files 6 ## input files
6 -b $input1 7 -b $input1
7 -t $input2 8 -t $input2
25 #else: 26 #else:
26 -n "Unspecified" 27 -n "Unspecified"
27 #end if 28 #end if
28 </command> 29 </command>
29 <requirements> 30 <requirements>
30 <requirement type="package">BEDTools</requirement> 31 <requirement type="package" version="2.11.0">R</requirement>
31 <requirement type="package">samtools</requirement> 32 <requirement type="package" version="2.18.2">bedtools</requirement>
33 <requirement type="package" version="0.1.18">samtools</requirement>
32 <requirement type="binary">pdflatex</requirement> 34 <requirement type="binary">pdflatex</requirement>
33 </requirements> 35 </requirements>
34 <inputs> 36 <inputs>
35 <param name="input1" type="data" format="bam" label="BAM file" help="BAM file of mapped reads" /> 37 <param name="input1" type="data" format="bam" label="BAM file" help="BAM file of mapped reads" />
36 <param name="input2" type="data" format="bed" label="Target Regions BED" help="BED file containing regions of interest. See below for format" /> 38 <param name="input2" type="data" format="bed" label="Target Regions BED" help="BED file containing regions of interest. See below for format" />
78 The BED file containing targets of interest has very specific format requirements. You **must** use the following format:: 80 The BED file containing targets of interest has very specific format requirements. You **must** use the following format::
79 81
80 Column 1: Chromosome : Use the same syntax as the references used by Galaxy. Check your sam-headers for the correct format. ('chr1' vs '1') 82 Column 1: Chromosome : Use the same syntax as the references used by Galaxy. Check your sam-headers for the correct format. ('chr1' vs '1')
81 Column 2: Start Position 83 Column 2: Start Position
82 Column 3: End Position 84 Column 3: End Position
83 Column 4: Target Name. Use : "GENE-NAME|Exon_number" : This is split on the 'Pipe' after 'GeneName' for correct grouping. 85 Column 4: Target Name. Use : "GENE-NAME&lt;space&gt;Exon_number" : This is split on the space after 'GeneName' for correct grouping.
84 Column 5: Score : ignored, use '0' 86 Column 5: Score : ignored, use '0'
85 Column 6: Strand: ignored,'+' or '-' 87 Column 6: Strand: ignored,'+' or '-'
86 88
87 .. class:: infomark 89 .. class:: infomark
88 90
109 111
110 **Targets.Position.Coverage** : Original BED file + following columns:: 112 **Targets.Position.Coverage** : Original BED file + following columns::
111 - Position in target region 113 - Position in target region
112 - Coverage at position 114 - Coverage at position
113 115
114 ------
115
116 **Requirements**
117
118 - BEDTools (from toolshed)
119 - Samtools (from toolshed)
120 - pdflatex : binary must be in path, to create the pdf report.
121
122 </help> 116 </help>
123 </tool> 117 </tool>
124 118
125 119