Mercurial > repos > iuc > chira_quantify

comparison chira_quantify.xml @ 10:7d46a32774ae draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 51f68a6d51d9e87f8e54021ce760b1506a3589b8"
author iuc
date Sun, 14 Jun 2020 21:33:42 +0000
parents 5f9b51cc2b4f
children ce47140889db
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9:5f452123d455 10:7d46a32774ae
23 <param name="min_locus_size" type="integer" value="10" 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="0.1" label="EM threshold"
29 help="The maximum difference of transcripts expression between two consecutive iterations of EM algorithm to converge."/> 29 help="The maximum difference of transcripts expression between two consecutive iterations of EM algorithm to converge."/>
30 <param name="crl" type="boolean" truevalue="-crl" falsevalue="" checked="true" 30 <param name="crl" type="boolean" truevalue="-crl" falsevalue="" checked="true"
31 label="Create CRLs" help="Create CRLs and qunatify them or use the loci further without creating the CRLs" /> 31 label="Create CRLs" help="Create CRLs and qunatify them or use the loci further without creating the CRLs" />
32 </inputs> 32 </inputs>
33 <outputs> 33 <outputs>
35 </outputs> 35 </outputs>
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="em_threshold" value="1"/>
40 <param name="merged" value="merged.bed"/> 41 <param name="merged" value="merged.bed"/>
41 <param name="min_locus_size" value="5"/> 42 <param name="min_locus_size" value="5"/>
42 <output name="loci" file="loci.counts"/> 43 <output name="loci" file="loci.counts"/>
43 </test> 44 </test>
44 </tests> 45 </tests>