Mercurial > repos > iuc > chira_quantify
comparison chira_quantify.xml @ 8:e40017f9cff1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"
| author | iuc |
|---|---|
| date | Fri, 29 May 2020 06:57:28 -0400 |
| parents | 2b150f2a012b |
| children | e0f08a05b24c |
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| 7:a1694947910f | 8:e40017f9cff1 |
|---|---|
| 18 <inputs> | 18 <inputs> |
| 19 <param format="bed" name="segments" type="data" label="BED file of aligned segments"/> | 19 <param format="bed" name="segments" type="data" label="BED file of aligned segments"/> |
| 20 <param format="tabular" name="merged" type="data" label="Tabular file of merged alignments"/> | 20 <param format="tabular" name="merged" type="data" label="Tabular file of merged alignments"/> |
| 21 <param name="crl_share" type="float" value="0.7" label="CRL locus fraction" min="0" max="1" | 21 <param name="crl_share" type="float" value="0.7" label="CRL locus fraction" min="0" max="1" |
| 22 help="Minimum fraction of reads of a locus that must overlap with all CRL loci inorder to merge itinto that CRL."/> | 22 help="Minimum fraction of reads of a locus that must overlap with all CRL loci inorder to merge itinto that CRL."/> |
| 23 <param name="min_locus_size" type="integer" value="5" label="Minimum locus size" min="1" | 23 <param name="min_locus_size" type="integer" value="10" label="Minimum locus size" min="1" |
| 24 help="Minimum number of reads a locus should have in order to participate in CRL creation. | 24 help="Minimum number of reads a locus should have in order to participate in CRL creation. |
| 25 Always set this value relative to your sequencing depth. Setting this to lower leads | 25 Always set this value relative to your sequencing depth. Setting this to lower leads |
| 26 CRLs of random multimappings Also consider setting the --crl_share option | 26 CRLs of random multimappings Also consider setting the --crl_share option |
| 27 along with this"/> | 27 along with this"/> |
| 28 <param name="em_threshold" type="float" value="1" label="EM threshold" | 28 <param name="em_threshold" type="float" value="1" label="EM threshold" |
| 36 | 36 |
| 37 <tests> | 37 <tests> |
| 38 <test expect_num_outputs="1"> | 38 <test expect_num_outputs="1"> |
| 39 <param name="segments" value="segments.bed"/> | 39 <param name="segments" value="segments.bed"/> |
| 40 <param name="merged" value="merged.bed"/> | 40 <param name="merged" value="merged.bed"/> |
| 41 <param name="min_locus_size" value="5"/> | |
| 41 <output name="loci" file="loci.counts"/> | 42 <output name="loci" file="loci.counts"/> |
| 42 </test> | 43 </test> |
| 43 </tests> | 44 </tests> |
| 44 | 45 |
| 45 <help> | 46 <help> |