Mercurial > repos > iuc > samtools_view
comparison macros.xml @ 7:b01db2684fa5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
| author | iuc |
|---|---|
| date | Tue, 21 Jan 2020 07:40:18 -0500 |
| parents | b91e0f76afe9 |
| children | 350bbc5c2ffd |
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| 6:ff313de5f7f4 | 7:b01db2684fa5 |
|---|---|
| 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[ |