Mercurial > repos > trinity_ctat > ctat_lncrna
comparison ctat_lncrna.xml @ 3:80b2cedf1a6f draft
Uploaded
| author | trinity_ctat |
|---|---|
| date | Thu, 21 Jun 2018 19:02:30 -0400 |
| parents | 5be72b8acec1 |
| children | 2847714632d9 |
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| 2:f3ab44021b9d | 3:80b2cedf1a6f |
|---|---|
| 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> |