Mercurial > repos > petr-novak > re_utils

comparison ChipSeqRatioDef.xml @ 6:f224513123a1 draft

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author petr-novak
date Mon, 02 Dec 2019 03:45:28 -0500
parents e320ef2d105a
children 89c5ba120b21
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5:378565f5a875 6:f224513123a1
5 <description></description> 5 <description></description>
6 <requirements> 6 <requirements>
7 <requirement type="package">r-base64enc</requirement> 7 <requirement type="package">r-base64enc</requirement>
8 <requirement type="package">r-r2html</requirement> 8 <requirement type="package">r-r2html</requirement>
9 <requirement type="package">blast</requirement> 9 <requirement type="package">blast</requirement>
10 <!-- <requirement type="package">chip_seq_ration</requirement> -->
10 </requirements> 11 </requirements>
11 <command interpreter="python3"> 12 <command interpreter="python3">
12 ChipSeqRatioAnalysis.py 13 ChipSeqRatioAnalysis.py
13 --ChipSeq=${ChipFile} 14 --ChipSeq=${ChipFile}
14 --InputSeq=${InputFile} 15 --InputSeq=${InputFile}
24 <param name="ChipFile" label="Chip Sequences" type="data" format="fasta" help="NGS data in fasta format"/> 25 <param name="ChipFile" label="Chip Sequences" type="data" format="fasta" help="NGS data in fasta format"/>
25 <param name="InputFile" label="Input Sequences" type="data" format="fasta" help="NGS data in fasta format"/> 26 <param name="InputFile" label="Input Sequences" type="data" format="fasta" help="NGS data in fasta format"/>
26 <param name="ContigFile" label="Reference - Contig Sequences" type="data" format="fasta" 27 <param name="ContigFile" label="Reference - Contig Sequences" type="data" format="fasta"
27 help="Contigs obtained from RepeatExplorer clustering pipeline in fasta file"/> 28 help="Contigs obtained from RepeatExplorer clustering pipeline in fasta file"/>
28 <param name="MaxCl" label="Number of clusters to be shown in graph" type="integer" value="200"/> 29 <param name="MaxCl" label="Number of clusters to be shown in graph" type="integer" value="200"/>
29 <param name="bitscore" label="Minimum bit score threshold" type="integer" value="30" help="All similarity hits with lower bit score will not be considered for ChIP/Input ratio calculation"/> 30 <param name="bitscore" label="Minimum bit score threshold" type="integer" value="50" help="All similarity hits with lower bit score will not be considered for ChIP/Input ratio calculation"/>
30 </inputs> 31 </inputs>
31 <outputs> 32 <outputs>
32 <data name="OutputFile" format="tabular"/> 33 <data name="OutputFile" format="tabular"/>
33 <data name="ReportFile" format="html"/> 34 <data name="ReportFile" format="html"/>
34 </outputs> 35 </outputs>