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comparison CoverageReport.xml @ 19:6c7b09220992 draft

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new version 0.0.3 (fix on headless R)
author geert-vandeweyer
date Thu, 06 Nov 2014 03:35:57 -0500
parents 43427b07e6bb
children b8e4ed167120
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18:43427b07e6bb 19:6c7b09220992
1 <tool id="CoverageReport2" name="Panel Coverage Report" version="0.0.2"> 1 <tool id="CoverageReport2" name="Panel Coverage Report" version="0.0.3">
2 <description></description> 2 <description></description>
3 3
4 <command interpreter="perl"> 4 <command interpreter="perl">
5 CoverageReport.pl 5 CoverageReport.pl
6 ## input files 6 ## input files
79 The BED file containing targets of interest has very specific format requirements. You **must** use the following format:: 79 The BED file containing targets of interest has very specific format requirements. You **must** use the following format::
80 80
81 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 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 2: Start Position 82 Column 2: Start Position
83 Column 3: End Position 83 Column 3: End Position
84 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 4: Target Name. Use : "GENE-NAME|Exon_number" : This is split on the pipe (or space) after 'GeneName' for correct grouping.Example: "CLIP2|Exon_4"
85 Column 5: Score : ignored, use '0' 85 Column 5: Score : ignored, use '0'
86 Column 6: Strand: ignored,'+' or '-' 86 Column 6: Strand: ignored,'+' or '-'
87 87
88 .. class:: infomark 88 .. class:: infomark
89 89