Mercurial > repos > trinity_ctat > ctat_lncrna
comparison ctat_lncrna.xml @ 9:f4fe52ab2ead draft
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author | trinity_ctat |
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date | Tue, 03 Jul 2018 10:52:16 -0400 |
parents | bddb36ef9fb3 |
children | f3f722c9dbf8 |
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8:bddb36ef9fb3 | 9:f4fe52ab2ead |
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6 </requirements> | 6 </requirements> |
7 <command detect_errors="default"> | 7 <command detect_errors="default"> |
8 <![CDATA[ | 8 <![CDATA[ |
9 #if str($bedfile) != "": | 9 #if str($bedfile) != "": |
10 lncrna --bedfile $bedfile | 10 lncrna --bedfile $bedfile |
11 --config "${annotations.fields.path}" | 11 --config "${assembly.fields.path}" |
12 #end if | 12 #end if |
13 | 13 |
14 #if str($assembly) != "": | 14 #if str($assembly) != "": |
15 --assembly "$assembly" | 15 --assembly "${assembly.fields.value}" |
16 #end if | 16 #end if |
17 | 17 |
18 #if $min_overlap != "": | 18 #if $min_overlap != "": |
19 --min_overlap "$min_overlap" | 19 --min_overlap "$min_overlap" |
20 #end if | 20 #end if |
55 <param name="min_coding" type="float" value="0.1" label="Min exonic identity to filter out transcript that aligns to orthologous coding gene" help="default is set by learning coding alignment distribution from data"/> | 55 <param name="min_coding" type="float" value="0.1" label="Min exonic identity to filter out transcript that aligns to orthologous coding gene" help="default is set by learning coding alignment distribution from data"/> |
56 <param name="minMatch" type="float" value="0.1" label="Min match" help="Minimum match parameter for liftover" /> | 56 <param name="minMatch" type="float" value="0.1" label="Min match" help="Minimum match parameter for liftover" /> |
57 <param name="pad" type="integer" value="0" label="Pad" help="No. of basepairs to search up- and down-stream when lifting over lnc to ortholog" /> | 57 <param name="pad" type="integer" value="0" label="Pad" help="No. of basepairs to search up- and down-stream when lifting over lnc to ortholog" /> |
58 <param name="gap_open" type="text" value="200" label="Gap open penalty to pass to lastz" help="Decreasing this parameter will increase sensitivity of orthology search"/> | 58 <param name="gap_open" type="text" value="200" label="Gap open penalty to pass to lastz" help="Decreasing this parameter will increase sensitivity of orthology search"/> |
59 <param name="gap_extend" type="text" value="40" label="Gap extend penalty to pass to lastz" help="Decreasing this parameter will increase sensitivity of orthology search."/> | 59 <param name="gap_extend" type="text" value="40" label="Gap extend penalty to pass to lastz" help="Decreasing this parameter will increase sensitivity of orthology search."/> |
60 <param name="annotations" type="select" label="Choose annotation:" help="Select annotation"> | 60 <param name="assembly" type="select" label="Choose annotation:" help="Select annotation"> |
61 <options from_data_table="ctat_lncrna_annotations" /> | 61 <options from_data_table="ctat_lncrna_annotations" /> |
62 </param> | 62 </param> |
63 </inputs> | 63 </inputs> |
64 | 64 |
65 <outputs> | 65 <outputs> |