Mercurial > repos > iuc > stringtie
comparison stringtie.xml @ 1:ab4798cf6458 draft
Uploaded
| author | iuc |
|---|---|
| date | Wed, 18 Feb 2015 11:37:10 -0500 |
| parents | f5c030adcded |
| children | b9c548ed919f |
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| 0:f5c030adcded | 1:ab4798cf6458 |
|---|---|
| 45 </param> | 45 </param> |
| 46 <when value="default" /> | 46 <when value="default" /> |
| 47 <when value="advanced"> | 47 <when value="advanced"> |
| 48 <param name="disable_trimming" type="boolean" falsevalue="" truevalue="-t" label="Disable trimming of predicted transcripts based on coverage" /> | 48 <param name="disable_trimming" type="boolean" falsevalue="" truevalue="-t" label="Disable trimming of predicted transcripts based on coverage" /> |
| 49 <param name="sensitive" type="boolean" truevalue="-S" falsevalue="" label="Increase sensitivity" /> | 49 <param name="sensitive" type="boolean" truevalue="-S" falsevalue="" label="Increase sensitivity" /> |
| 50 <param name="label" type="text" value="STRG" label="Name prefix for output transcripts" /> | |
| 51 <param name="fraction" type="float" value="0.15" min="0.0" max="1.0" label="Minimum isoform fraction" /> | 50 <param name="fraction" type="float" value="0.15" min="0.0" max="1.0" label="Minimum isoform fraction" /> |
| 52 <param name="min_tlen" type="integer" value="200" label="Minimum assembled transcript length" /> | 51 <param name="min_tlen" type="integer" value="200" label="Minimum assembled transcript length" /> |
| 53 <param name="min_anchor_len" type="integer" value="10" label="Minimum anchor length for junctions" /> | 52 <param name="min_anchor_len" type="integer" value="10" label="Minimum anchor length for junctions" /> |
| 54 <param name="min_anchor_cov" type="integer" value="1" label="Minimum junction coverage" /> | 53 <param name="min_anchor_cov" type="integer" value="1" label="Minimum junction coverage" /> |
| 55 <param name="min_bundle_cov" type="integer" value="2" label="Minimum bundle reads per bp coverage to consider for assembly" /> | 54 <param name="min_bundle_cov" type="integer" value="2" label="Minimum bundle reads per bp coverage to consider for assembly" /> |
| 101 -t disable trimming of predicted transcripts based on coverage (default: trimming enabled) | 100 -t disable trimming of predicted transcripts based on coverage (default: trimming enabled) |
| 102 -c minimum bundle reads per bp coverage to consider for assembly (default: 2) | 101 -c minimum bundle reads per bp coverage to consider for assembly (default: 2) |
| 103 -s coverage saturation threshold; further read alignments will be | 102 -s coverage saturation threshold; further read alignments will be |
| 104 ignored in a region where a local coverage depth of <maxcov> | 103 ignored in a region where a local coverage depth of <maxcov> |
| 105 is reached (default: 1,000,000); | 104 is reached (default: 1,000,000); |
| 106 -v verbose (log bundle processing details) | |
| 107 -e abundance estimation only of input transcripts (for -G option) | 105 -e abundance estimation only of input transcripts (for -G option) |
| 108 -g gap between read mappings triggering a new bundle (default: 50) | 106 -g gap between read mappings triggering a new bundle (default: 50) |
| 109 -S more sensitive run (default: no) | 107 -S more sensitive run (default: no) |
| 110 -C output file with all transcripts in reference that are fully | 108 -C output file with all transcripts in reference that are fully |
| 111 covered by reads | 109 covered by reads |
| 112 -M fraction of bundle allowed to be covered by multi-hit reads (default:0.95) | 110 -M fraction of bundle allowed to be covered by multi-hit reads (default:0.95) |
| 113 -p number of threads (CPUs) to use (default: 1) | |
| 114 | 111 |
| 115 ]]> | 112 ]]> |
| 116 </help> | 113 </help> |
| 117 </tool> | 114 </tool> |