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comparison samtool_filter2.xml @ 2:886b73f04847 draft

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planemo upload commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
author devteam
date Fri, 09 Oct 2015 17:24:03 -0400
parents 94d5786febc4
children c31a37f6d48a
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1:94d5786febc4 2:886b73f04847
108 <option value="0x0200">The read fails platform/vendor quality checks</option> 108 <option value="0x0200">The read fails platform/vendor quality checks</option>
109 <option value="0x0400">The read is a PCR or optical duplicate</option> 109 <option value="0x0400">The read is a PCR or optical duplicate</option>
110 </param> 110 </param>
111 </when> 111 </when>
112 </conditional> 112 </conditional>
113 <param name="library" type="text" value="" size="20" label="Select alignments from Library" 113 <param name="library" type="text" value="" label="Select alignments from Library"
114 help="(-l) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/> 114 help="(-l) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/>
115 <param name="read_group" type="text" value="" size="20" label="Select alignments from Read Group" 115 <param name="read_group" type="text" value="" label="Select alignments from Read Group"
116 help="(-r) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/> 116 help="(-r) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/>
117 <param name="bed_file" type="data" format="bed" optional="true" label="Output alignments overlapping the regions in the BED FILE" help="(-L)"/> 117 <param name="bed_file" type="data" format="bed" optional="true" label="Output alignments overlapping the regions in the BED FILE" help="(-L)"/>
118 <param name="regions" type="text" value="" size="180" label="Select regions (only used when the input is in BAM format)" 118 <param name="regions" type="text" value="" label="Select regions (only used when the input is in BAM format)"
119 help="region should be presented in one of the following formats: `chr1', `chr2:1,000' and `chr3:1000-2,000'"/> 119 help="region should be presented in one of the following formats: `chr1', `chr2:1,000' and `chr3:1000-2,000'"/>
120 <param name="outputtype" type="select" label="Select the output format"> 120 <param name="outputtype" type="select" label="Select the output format">
121 <option value="bam">BAM (-b)</option> 121 <option value="bam">BAM (-b)</option>
122 <option value="sam">SAM</option> 122 <option value="sam">SAM</option>
123 </param> 123 </param>