Mercurial > repos > iuc > nanocompore_db

annotate nanocompore_db.xml @ 2:d193d0e411bd draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 07:47:15 +0000
parents 97a6b3f9a98d
children
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1 <tool id="nanocompore_db" name="NanoComporeDB" version="@TOOL_VERSION@+galaxy2">
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2 <description>Process SampComp results database</description>
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 mkdir -p results plots &&
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10 tar -xf '$db' --strip-components 1 -C results/ &&
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11 python '$__tool_directory__/NanocomporeDB_process.py'
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12 --db-path 'results/out_SampComp.db'
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13 --ref-fasta '$reference'
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14 --annotation-bed '$annotation'
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15 --pvalue-types '$pvalue_types'
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16 --pvalue-threshold $pvalue_threshold
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17 --out-dir ./plots/
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18 $bedgraph
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19
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20 ]]></command>
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21 <inputs>
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22 <param name="reference" type="data" format="fasta" label="The reference genome used for read alignment."/>
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23 <param name="annotation" format="bed" type="data" label="BED file containing the annotation of the transcriptome used as reference when mapping"/>
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24 <param name="db" type="data" format="tar" label="SampComp Database" />
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25 <param argument="--pvalue-types" type="text" value="GMM_logit_pvalue,KS_dwell_pvalue,KS_intensity_pvalue" label="pvalue field names" help="Comma-separated values.">
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26 <validator type="regex" message="No valid pvalue field name list.">^(\w+(,\w+)*)?$</validator>
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27 </param>
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28 <param argument="pvalue-threshold" type="float" value="1.0" min="0.0" label="Maximum reported p-value"/>
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29 <param argument="--bedgraph" type="boolean" truevalue="--bedgraph" falsevalue="" label="Write output in BedGraph format instead of BED"/>
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30 </inputs>
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31 <outputs>
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32 <collection name="pvalue_output" type="list">
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33 <discover_datasets pattern="__name_and_ext__" directory="plots" />
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34 </collection>
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="reference" value="reference.fa"/>
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39 <param name="annotation" value="annot.bed"/>
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40 <param name="db" value="DB.tar" ftype="tar" />
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41 <output_collection name="pvalue_output" type="list" count="3">
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42 <element name="GMM_logit_pvalue" file="GMM_logit_pvalue.bed" ftype="bed"/>
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43 <element name="KS_dwell_pvalue" file="KS_dwell_pvalue.bed" ftype="bed"/>
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44 <element name="KS_intensity_pvalue" file="KS_intensity_pvalue.bed" ftype="bed"/>
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45 </output_collection>
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46 </test>
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47 <test>
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48 <param name="reference" value="reference.fa"/>
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49 <param name="annotation" value="annot.bed"/>
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50 <param name="db" value="DB.tar" ftype="tar" />
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51 <param name="bedgraph" value="true"/>
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52 <param name="pvalue_types" value="GMM_logit_pvalue,KS_dwell_pvalue"/>
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53 <output_collection name="pvalue_output" type="list" count="2">
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54 <element name="GMM_logit_pvalue" file="GMM_logit_pvalue.bedgraph" ftype="bedgraph"/>
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55 <element name="KS_dwell_pvalue" file="KS_dwell_pvalue.bedgraph" ftype="bedgraph"/>
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56 </output_collection>
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57 </test>
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58 </tests>
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59 <help><![CDATA[
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60 Produces interval bed and bedgraph outputs from NanoCompore SampComp results as input using NaonComporeDB API.
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61
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62 **References**
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63
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64 @REFERENCES@
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65 ]]></help>
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66 <expand macro="citations"/>
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67 </tool>