Mercurial > repos > iuc > samtools_cram_to_bam

comparison macros.xml @ 3:858ada516d8f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 9aed35e37c5bc8ee17a02930c1f2edceb8b0d97b"
author iuc
date Sat, 31 Jul 2021 07:26:19 +0000
parents d459230531aa
children 1551b0dd2d16
comparison
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2:a744bb7196a2 3:858ada516d8f
75 ]]></token> 75 ]]></token>
76 <xml name="seed_input"> 76 <xml name="seed_input">
77 <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> 77 <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." />
78 </xml> 78 </xml>
79 <xml name="flag_options"> 79 <xml name="flag_options">
80 <option value="1">read is paired</option> 80 <option value="1">Read is paired</option>
81 <option value="2">read is mapped in a proper pair</option> 81 <option value="2">Read is mapped in a proper pair</option>
82 <option value="4">read is unmapped</option> 82 <option value="4">Read is unmapped</option>
83 <option value="8">mate is unmapped</option> 83 <option value="8">Mate is unmapped</option>
84 <option value="16">read reverse strand</option> 84 <option value="16">Read is mapped to the reverse strand of the reference</option>
85 <option value="32">mate reverse strand</option> 85 <option value="32">Mate is mapped to the reverse strand of the reference</option>
86 <option value="64">read is the first in a pair</option> 86 <option value="64">Read is the first in a pair</option>
87 <option value="128">read is the second in a pair</option> 87 <option value="128">Read is the second in a pair</option>
88 <option value="256">alignment or read is not primary</option> 88 <option value="256">Alignment of the read is not primary</option>
89 <option value="512">read fails platform/vendor quality checks</option> 89 <option value="512">Read fails platform/vendor quality checks</option>
90 <option value="1024">read is a PCR or optical duplicate</option> 90 <option value="1024">Read is a PCR or optical duplicate</option>
91 <option value="2048">supplementary alignment</option> 91 <option value="2048">Alignment is supplementary</option>
92 </xml> 92 </xml>
93 93
94 <!-- region specification macros and tokens for tools that allow the specification 94 <!-- region specification macros and tokens for tools that allow the specification
95 of region by bed file / space separated list of regions --> 95 of region by bed file / space separated list of regions -->
96 <token name="@REGIONS_FILE@"><![CDATA[ 96 <token name="@REGIONS_FILE@"><![CDATA[