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comparison htseqsams2mx.xml @ 64:d300bc688e95 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit e5a5ad091c621348dc6ce2df861475ebc54a380e
author iuc
date Tue, 13 Oct 2015 17:24:08 -0400
parents 57841366f112
children
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63:e34313b3898b 64:d300bc688e95
19 #if $filter_extras: 19 #if $filter_extras:
20 --filter_extras "$filter_extras" 20 --filter_extras "$filter_extras"
21 #end if 21 #end if
22 </command> 22 </command>
23 <inputs> 23 <inputs>
24 <param format="gtf" name="gfffile" type="data" label="Gene model (GFF) file to count reads over from your current history" size="100" /> 24 <param format="gtf" name="gfffile" type="data" label="Gene model (GFF) file to count reads over from your current history" />
25 <param name="mapqMin" label="Filter reads with mapq below than this value" 25 <param name="mapqMin" label="Filter reads with mapq below than this value"
26 help="0 to count any mapping quality read. Otherwise only reads at or above specified mapq will be counted" 26 help="0 to count any mapping quality read. Otherwise only reads at or above specified mapq will be counted"
27 type="integer" value="5"/> 27 type="integer" value="5"/>
28 <param name="title" label="Name for this job's output file" type="text" size="80" value="bams to DGE count matrix"/> 28 <param name="title" label="Name for this job's output file" type="text" value="bams to DGE count matrix"/>
29 <param name="stranded" value="false" type="boolean" label="Reads are stranded - use strand in counting" display="checkbox" 29 <param name="stranded" value="false" type="boolean" label="Reads are stranded - use strand in counting" display="checkbox"
30 truevalue="yes" falsevalue="no" checked="no" help="Check this ONLY if you know your sequences are strand specific" /> 30 truevalue="yes" falsevalue="no" checked="no" help="Check this ONLY if you know your sequences are strand specific" />
31 <param name="model" type="select" label="Model for counting reads over the supplied gene model- see HTSeq docs" 31 <param name="model" type="select" label="Model for counting reads over the supplied gene model- see HTSeq docs"
32 help="If in doubt, union is a reasonable default but intersection-strict avoids double counting over overlapping exons"> 32 help="If in doubt, union is a reasonable default but intersection-strict avoids double counting over overlapping exons">
33 <option value="union" selected="true">union</option> 33 <option value="union" selected="true">union</option>
53 <option value="">None</option> 53 <option value="">None</option>
54 <option value="XS">XS:i > 0 - More than one mapping position Bowtie</option> 54 <option value="XS">XS:i > 0 - More than one mapping position Bowtie</option>
55 <option value="XS:A">Might be useful for tophat</option> 55 <option value="XS:A">Might be useful for tophat</option>
56 </param> 56 </param>
57 57
58 <param name="samfiles" type="data" label="bam/sam file from your history" format="sam,bam" size="100" multiple="true"/> 58 <param name="samfiles" type="data" label="bam/sam file from your history" format="sam,bam" multiple="true"/>
59 </inputs> 59 </inputs>
60 <outputs> 60 <outputs>
61 <data format="tabular" name="outfile" label="${title}_htseqsams2mx.xls" /> 61 <data format="tabular" name="outfile" label="${title}_htseqsams2mx.xls" />
62 </outputs> 62 </outputs>
63 <tests> 63 <tests>