Mercurial > repos > cpt > cpt_xmfa_split
comparison cpt_xmfa_split/lcb_split.xml @ 0:21d00cf83137 draft
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| author | cpt |
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| date | Tue, 05 Jul 2022 05:19:47 +0000 |
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| -1:000000000000 | 0:21d00cf83137 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="edu.tamu.cpt.xmfa.split" name="Split LCBs into smaller LCBs" version="@WRAPPER_VERSION@.0"> | |
| 3 <description></description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 <import>cpt-macros.xml</import> | |
| 7 </macros> | |
| 8 <expand macro="requirements"/> | |
| 9 <command detect_errors="aggressive"><![CDATA[ | |
| 10 python $__tool_directory__/lcb_split.py | |
| 11 @XMFA_INPUT@ | |
| 12 --window_size $window_size | |
| 13 --threshold $threshold | |
| 14 > $output | |
| 15 ]]></command> | |
| 16 <inputs> | |
| 17 <expand macro="xmfa_input" /> | |
| 18 <param type="integer" name="window_size" value="10" label="Default window size generating smaller LCBs" /> | |
| 19 <param type="float" name="threshold" value="0.7" min="0" max="1" label="Threshold at which a given genome is part of the new small LCBs" /> | |
| 20 </inputs> | |
| 21 <outputs> | |
| 22 <data format="xmfa" name="output" /> | |
| 23 </outputs> | |
| 24 <help><![CDATA[ | |
| 25 **What it does** | |
| 26 | |
| 27 Helps reduce large and non-sensical protein LCBs into real protein alignments. | |
| 28 | |
| 29 **WARNING** | |
| 30 | |
| 31 Probably does not work if you have - strand genes. Need to test. | |
| 32 | |
| 33 ]]></help> | |
| 34 <!-- TODO --> | |
| 35 <expand macro="citations" /> | |
| 36 </tool> |