Mercurial > repos > iuc > nanocompore_db

annotate nanocompore_db.xml @ 1:97a6b3f9a98d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit a57b5b935a80db12a0ed867b4219453a2854dd32"
author iuc
date Wed, 17 Jun 2020 17:27:33 +0000
parents ace1c453a190
children d193d0e411bd
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97a6b3f9a98d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit a57b5b935a80db12a0ed867b4219453a2854dd32"
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1 <tool id="nanocompore_db" name="NanoComporeDB" version="@TOOL_VERSION@+galaxy1">
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2 <description>Process SampComp results database</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 mkdir results &&
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9 tar -xf $db --strip-components 1 -C results/ &&
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10 python '$__tool_directory__/NanocomporeDB_process.py'
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11 --db-path 'results/out_SampComp.db'
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12 --ref-fasta '$reference'
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13 --annotation-bed '$annotation'
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14 $bedgraph
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15 ]]></command>
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16 <inputs>
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17 <param name="reference" type="data" format="fasta" label="The reference genome used for read alignment."/>
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18 <param name="annotation" format="bed" type="data" label="BED file containing the annotation of the transcriptome used as reference when mapping"/>
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19 <param name="db" type="data" format="tar" label="SampComp Database" />
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20 <param argument="--bedgraph" type="boolean" truevalue="--bedgraph" falsevalue="" label="Write output in BEDGRAPH format instead of BED"/>
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21 </inputs>
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22 <outputs>
1
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23 <data name="GMM_logit" format="bed" from_work_dir="GMM_logit_pvalue.bedgraph" label="${tool.name} on ${on_string}: GMM_logit">
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24 <change_format>
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25 <when input="bedgraph" value="true" format="bedgraph"/>
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26 </change_format>
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27 </data>
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28
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29 <data name="KS_dwell" format="bed" from_work_dir="KS_dwell_pvalue.bedgraph" label="${tool.name} on ${on_string}: KS_dwell">
97a6b3f9a98d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit a57b5b935a80db12a0ed867b4219453a2854dd32"
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30 <change_format>
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31 <when input="bedgraph" value="true" format="bedgraph"/>
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32 </change_format>
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33 </data>
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34
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35 <data name="KS_intensity" format="bed" from_work_dir="KS_intensity_pvalue.bedgraph" label="${tool.name} on ${on_string}: KS_intensity">
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36 <change_format>
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37 <when input="bedgraph" value="true" format="bedgraph"/>
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38 </change_format>
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39 </data>
0
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="reference" value="reference.fa"/>
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44 <param name="annotation" value="annot.bed"/>
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45 <param name="db" value="DB.tar"/>
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46 <output name="GMM_logit" file="GMM_logit_pvalue.bed"/>
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47 <output name="KS_dwell" file="KS_dwell_pvalue.bed"/>
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48 <output name="KS_intensity" file="KS_intensity_pvalue.bed"/>
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49 </test>
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50 <test>
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51 <param name="reference" value="reference.fa"/>
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52 <param name="annotation" value="annot.bed"/>
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53 <param name="db" value="DB.tar"/>
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54 <param name="bedgraph" value="true"/>
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55 <output name="GMM_logit" file="GMM_logit_pvalue.bedgraph"/>
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56 <output name="KS_dwell" file="KS_dwell_pvalue.bedgraph"/>
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57 <output name="KS_intensity" file="KS_intensity_pvalue.bedgraph"/>
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58 </test>
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59 </tests>
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60 <help><![CDATA[
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61 Produces interval bed and bedgraph outputs from NanoCompore SampComp results as input using NaonComporeDB API.
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62
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63 **References**
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64
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65 @REFERENCES@
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66 ]]></help>
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67 <expand macro="citations"/>
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68 </tool>