Mercurial > repos > iuc > chira_quantify
comparison chira_quantify.xml @ 0:f7cce908ef9f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
| author | iuc |
|---|---|
| date | Sun, 19 Jan 2020 21:27:15 +0000 |
| parents | |
| children | 34f790d4d085 |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:f7cce908ef9f |
|---|---|
| 1 <tool id="chira_quantify" name="ChiRA qauntify" version="@WRAPPER_VERSION@0"> | |
| 2 <description>quantify aligned loci to score the alignments</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <command><![CDATA[ | |
| 8 chira_quantify.py | |
| 9 -b '$segments' | |
| 10 -m '$merged' | |
| 11 -cs '$crl_share' | |
| 12 -ls '$min_locus_size' | |
| 13 -e '$em_threshold' | |
| 14 '$crl' | |
| 15 -o ./ | |
| 16 ]]></command> | |
| 17 | |
| 18 <inputs> | |
| 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"/> | |
| 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."/> | |
| 23 <param name="min_locus_size" type="integer" value="5" label="Minimum locus size" min="1" | |
| 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 | |
| 26 CRLs of random multimappings Also consider setting the --crl_share option | |
| 27 along with this"/> | |
| 28 <param name="em_threshold" type="float" value="1" label="EM threshold" | |
| 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" | |
| 31 label="Create CRLs" help="Create CRLs and qunatify them or use the loci further without creating the CRLs" /> | |
| 32 </inputs> | |
| 33 <outputs> | |
| 34 <data format="tabular" name="loci" from_work_dir="loci.counts" label="ChiRA quantified loci on ${on_string}"/> | |
| 35 </outputs> | |
| 36 | |
| 37 <tests> | |
| 38 <test expect_num_outputs="1"> | |
| 39 <param name="segments" value="segments.bed"/> | |
| 40 <param name="merged" value="merged.bed"/> | |
| 41 <output name="loci" file="loci.counts"/> | |
| 42 </test> | |
| 43 </tests> | |
| 44 | |
| 45 <help> | |
| 46 | |
| 47 .. class:: infomark | |
| 48 | |
| 49 **What it does** | |
| 50 | |
| 51 This tool first creates CRLS from merged BED file and quantifies them based on the mapped reads. | |
| 52 | |
| 53 **Inputs** | |
| 54 | |
| 55 * A BED file containing alignment segments | |
| 56 * A BED file containing merged alignments | |
| 57 | |
| 58 **Output** | |
| 59 | |
| 60 * Tabular file containing the reads and their CRLs with TPM values. | |
| 61 | |
| 62 </help> | |
| 63 <expand macro="citations" /> | |
| 64 </tool> |