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comparison 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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1:97a6b3f9a98d 2:d193d0e411bd
1 <tool id="nanocompore_db" name="NanoComporeDB" version="@TOOL_VERSION@+galaxy1"> 1 <tool id="nanocompore_db" name="NanoComporeDB" version="@TOOL_VERSION@+galaxy2">
2 <description>Process SampComp results database</description> 2 <description>Process SampComp results database</description>
3 <expand macro="bio_tools"/>
3 <macros> 4 <macros>
4 <import>macros.xml</import> 5 <import>macros.xml</import>
5 </macros> 6 </macros>
6 <expand macro="requirements"/> 7 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
8 mkdir results && 9 mkdir -p results plots &&
9 tar -xf $db --strip-components 1 -C results/ && 10 tar -xf '$db' --strip-components 1 -C results/ &&
10 python '$__tool_directory__/NanocomporeDB_process.py' 11 python '$__tool_directory__/NanocomporeDB_process.py'
11 --db-path 'results/out_SampComp.db' 12 --db-path 'results/out_SampComp.db'
12 --ref-fasta '$reference' 13 --ref-fasta '$reference'
13 --annotation-bed '$annotation' 14 --annotation-bed '$annotation'
15 --pvalue-types '$pvalue_types'
16 --pvalue-threshold $pvalue_threshold
17 --out-dir ./plots/
14 $bedgraph 18 $bedgraph
19
15 ]]></command> 20 ]]></command>
16 <inputs> 21 <inputs>
17 <param name="reference" type="data" format="fasta" label="The reference genome used for read alignment."/> 22 <param name="reference" type="data" format="fasta" label="The reference genome used for read alignment."/>
18 <param name="annotation" format="bed" type="data" label="BED file containing the annotation of the transcriptome used as reference when mapping"/> 23 <param name="annotation" format="bed" type="data" label="BED file containing the annotation of the transcriptome used as reference when mapping"/>
19 <param name="db" type="data" format="tar" label="SampComp Database" /> 24 <param name="db" type="data" format="tar" label="SampComp Database" />
20 <param argument="--bedgraph" type="boolean" truevalue="--bedgraph" falsevalue="" label="Write output in BEDGRAPH format instead of BED"/> 25 <param argument="--pvalue-types" type="text" value="GMM_logit_pvalue,KS_dwell_pvalue,KS_intensity_pvalue" label="pvalue field names" help="Comma-separated values.">
26 <validator type="regex" message="No valid pvalue field name list.">^(\w+(,\w+)*)?$</validator>
27 </param>
28 <param argument="pvalue-threshold" type="float" value="1.0" min="0.0" label="Maximum reported p-value"/>
29 <param argument="--bedgraph" type="boolean" truevalue="--bedgraph" falsevalue="" label="Write output in BedGraph format instead of BED"/>
21 </inputs> 30 </inputs>
22 <outputs> 31 <outputs>
23 <data name="GMM_logit" format="bed" from_work_dir="GMM_logit_pvalue.bedgraph" label="${tool.name} on ${on_string}: GMM_logit"> 32 <collection name="pvalue_output" type="list">
24 <change_format> 33 <discover_datasets pattern="__name_and_ext__" directory="plots" />
25 <when input="bedgraph" value="true" format="bedgraph"/> 34 </collection>
26 </change_format>
27 </data>
28
29 <data name="KS_dwell" format="bed" from_work_dir="KS_dwell_pvalue.bedgraph" label="${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>
40 </outputs> 35 </outputs>
41 <tests> 36 <tests>
42 <test> 37 <test>
43 <param name="reference" value="reference.fa"/> 38 <param name="reference" value="reference.fa"/>
44 <param name="annotation" value="annot.bed"/> 39 <param name="annotation" value="annot.bed"/>
45 <param name="db" value="DB.tar"/> 40 <param name="db" value="DB.tar" ftype="tar" />
46 <output name="GMM_logit" file="GMM_logit_pvalue.bed"/> 41 <output_collection name="pvalue_output" type="list" count="3">
47 <output name="KS_dwell" file="KS_dwell_pvalue.bed"/> 42 <element name="GMM_logit_pvalue" file="GMM_logit_pvalue.bed" ftype="bed"/>
48 <output name="KS_intensity" file="KS_intensity_pvalue.bed"/> 43 <element name="KS_dwell_pvalue" file="KS_dwell_pvalue.bed" ftype="bed"/>
44 <element name="KS_intensity_pvalue" file="KS_intensity_pvalue.bed" ftype="bed"/>
45 </output_collection>
49 </test> 46 </test>
50 <test> 47 <test>
51 <param name="reference" value="reference.fa"/> 48 <param name="reference" value="reference.fa"/>
52 <param name="annotation" value="annot.bed"/> 49 <param name="annotation" value="annot.bed"/>
53 <param name="db" value="DB.tar"/> 50 <param name="db" value="DB.tar" ftype="tar" />
54 <param name="bedgraph" value="true"/> 51 <param name="bedgraph" value="true"/>
55 <output name="GMM_logit" file="GMM_logit_pvalue.bedgraph"/> 52 <param name="pvalue_types" value="GMM_logit_pvalue,KS_dwell_pvalue"/>
56 <output name="KS_dwell" file="KS_dwell_pvalue.bedgraph"/> 53 <output_collection name="pvalue_output" type="list" count="2">
57 <output name="KS_intensity" file="KS_intensity_pvalue.bedgraph"/> 54 <element name="GMM_logit_pvalue" file="GMM_logit_pvalue.bedgraph" ftype="bedgraph"/>
58 </test> 55 <element name="KS_dwell_pvalue" file="KS_dwell_pvalue.bedgraph" ftype="bedgraph"/>
56 </output_collection>
57 </test>
59 </tests> 58 </tests>
60 <help><![CDATA[ 59 <help><![CDATA[
61 Produces interval bed and bedgraph outputs from NanoCompore SampComp results as input using NaonComporeDB API. 60 Produces interval bed and bedgraph outputs from NanoCompore SampComp results as input using NaonComporeDB API.
62 61
63 **References** 62 **References**