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