Mercurial > repos > arkarachai-fungtammasan > str_fm

comparison PEsortedSAM2readprofile.xml @ 13:35aedbe548b9 draft

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author arkarachai-fungtammasan
date Sun, 24 Jul 2016 17:56:49 -0400
parents d5ed5c2e25c3
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12:a3113043abb0 13:35aedbe548b9
1 <tool id="PEsortedSAM2readprofile" name="Combine mapped faux paired-end reads" version="1.0.0"> 1 <tool id="PEsortedSAM2readprofile" name="Combine mapped faux paired-end reads" version="1.1.0">
2 <description> and get the reference STR allele from the reference genome </description> 2 <description> and get the reference STR allele from the reference genome </description>
3 <command interpreter="python2.7">PEsortedSAM2readprofile.py $flankedbasesSAM $twobitref $maxTRlength $maxoriginalreadlength $output </command> 3 <command interpreter="python2.7">PEsortedSAM2readprofile.py $flankedbasesSAM $twobitref $maxTRlength $maxoriginalreadlength $output </command>
4 4
5 <inputs> 5 <inputs>
6 <param name="flankedbasesSAM" type="data" format="sam" label="Select sorted SAM file (by readname) of flaked bases" /> 6 <param name="flankedbasesSAM" type="data" format="sam" label="Select sorted SAM file (by readname) of flaked bases" />
7 <param name="twobitref" type="data" label="Select twobit file reference genome" /> 7 <param name="twobitref" type="data" label="Select twobit file reference genome" />
8 <param name="maxTRlength" type="integer" value="100" label="Maximum expected microsatellite length (bp)" /> 8 <param name="maxTRlength" type="integer" value="100" label="Maximum microsatellite length in reference (bp)" />
9 <param name="maxoriginalreadlength" type="integer" value="101" label="Maxinum original read length" /> 9 <param name="maxoriginalreadlength" type="integer" value="101" label="Maxinum original read length" />
10 10
11 </inputs> 11 </inputs>
12 <outputs> 12 <outputs>
13 <data name="output" format="tabular" /> 13 <data name="output" format="tabular" />