Mercurial > repos > yufei-luo > s_mart

comparison SMART/galaxy/mapperAnalyzer.xml @ 18:94ab73e8a190

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
parents 440ceca58672
children 0ab839023fe4
comparison
equal deleted inserted replaced
17:b0e8584489e6 18:94ab73e8a190
1 <tool id="mapperAnalyzer" name="mapper analyzer"> 1 <tool id="mapperAnalyzer" name="mapper analyzer">
2 <description>Read the output of an aligner, print statistics and possibly translate into GFF, BED or GBrowse formats. </description> 2 <description>Read the output of an aligner, print statistics and possibly translate into GFF, BED or GBrowse formats. </description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
3 <command interpreter="python"> 6 <command interpreter="python">
4 ../Java/Python/mapperAnalyzer.py -i $formatType.inputFileName1 7 ../Java/Python/mapperAnalyzer.py -i $formatType.inputFileName1
5 #if $formatType.FormatInputFileName1 == 'bed': 8 #if $formatType.FormatInputFileName1 == 'bed':
6 -f bed 9 -f bed
7 #elif $formatType.FormatInputFileName1 == 'gff3': 10 #elif $formatType.FormatInputFileName1 == 'gff3':
177 <param name="remove" type="boolean" truevalue="-x" falsevalue="" checked="false" label="remove transcripts when exons are short"/> 180 <param name="remove" type="boolean" truevalue="-x" falsevalue="" checked="false" label="remove transcripts when exons are short"/>
178 <param name="remain" type="boolean" truevalue="-r" falsevalue="" checked="false" label="print the unmatched sequences "/> 181 <param name="remain" type="boolean" truevalue="-r" falsevalue="" checked="false" label="print the unmatched sequences "/>
179 </inputs> 182 </inputs>
180 183
181 <outputs> 184 <outputs>
182 <data name="outputFileGFF" format="gff3" label="[mapperAnalyzer] out file"/> 185 <data name="outputFileGFF" format="gff3" label="[mapper analyzer] output file"/>
183 </outputs> 186 </outputs>
184 187
185 <help> 188 <help>
186 Maybe the first program you may use. It reads a set of mapping given by the tool you have used to map your data on the reference genome and translate it to a set of genomic coordinates. You also have the possibility to extract only those that you are interested in (few matches in the genome, few errors in the mapping, etc.). You can also select those reads which map less than a given of times in the genome. Moreover, you can output the data in various different formats, which you can use to visualize them *via* UCSC genome browser or GBrowse. Unmatched reads can be written in an other file, in case you would like to try to map them with another tool (may sometimes work!). 189 Maybe the first program you may use. It reads a set of mapping given by the tool you have used to map your data on the reference genome and translate it to a set of genomic coordinates. You also have the possibility to extract only those that you are interested in (few matches in the genome, few errors in the mapping, etc.). You can also select those reads which map less than a given of times in the genome. Moreover, you can output the data in various different formats, which you can use to visualize them *via* UCSC genome browser or GBrowse. Unmatched reads can be written in an other file, in case you would like to try to map them with another tool (may sometimes work!).
187 190