Mercurial > repos > recetox > riassigner

comparison riassigner.xml @ 1:97c0aae5eb69 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner commit 42ac00642f210eca50e3ee6b8b7548da6717a599"
author recetox
date Sat, 04 Sep 2021 14:03:58 +0000
parents 7cc615de435e
children 113f5f66e6b9
comparison
equal deleted inserted replaced
0:7cc615de435e 1:97c0aae5eb69
1 <tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5"> 1 <tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy0" profile="19.05">
2 <description>compute retention indices</description> 2 <description>compute retention indices</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">riassigner</requirement>
8 </requirements>
6 <expand macro="creator"/> 9 <expand macro="creator"/>
7 <expand macro="requirements" />
8 10
9 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
10 sh ${symlink_inputs} && 12 python -m RIAssigner --reference "$reference_section.reference" "$reference_section.reference.ext" "$reference_section.reference_rt_units" --query "$query_section.query" "$query_section.query.ext" "$query_section.query_rt_units" --method "$method" --output "output.${query_section.query.ext}" &&
11 python -m RIAssigner --reference "$reference.element_identifier" --query "$query.element_identifier" --method "$method" --output "output.${query.ext}" && 13 cp -r 'output.${query_section.query.ext}' '${output}'
12 cp -r 'output.${query.ext}' '${output}' 14 ]]>
13 ]]></command> 15 </command>
14
15 <configfiles>
16 <configfile name="symlink_inputs">
17 ln -s '${query}' '${query.element_identifier}'
18 ln -s '${reference}' '${reference.element_identifier}'
19 </configfile>
20 </configfiles>
21 16
22 <inputs> 17 <inputs>
23 <param name="reference" type="data" format="csv,tsv,msp"> 18 <section name="query_section" title="Query dataset" expanded="true">
24 <label>Reference compound list</label> 19 <param name="query" type="data" format="csv,tsv,msp">
25 <help><![CDATA[ 20 <label>Query compound list</label>
26 A list of retention time and retention index pairs. 21 <help><![CDATA[
27 Expected columns for RT (oneof): ['rt', 'retention_time'].
28 Expected columns for RI (oneof): ['carbon_number', 'ri', 'retention_index'].
29 Retention time is expected to be in seconds.
30 ]]></help>
31 </param>
32 <param name="query" type="data" format="csv,tsv,msp">
33 <label>Query compound list</label>
34 <help><![CDATA[
35 A list of compounds with retention times for which to compute the retention index. 22 A list of compounds with retention times for which to compute the retention index.
36 Expected columns for RT (oneof): ['rt', 'retention_time']. 23 Expected columns for RT (oneof): ['rt', 'retention_time'].
37 Retention time is expected to be in seconds.
38 ]]></help> 24 ]]></help>
39 </param> 25 </param>
26 <param name="query_rt_units" type="select" display="radio" help="Retention time units in the query file.">
27 <option value="seconds" selected="true">Seconds</option>
28 <option value="min">Minutes</option>
29 </param>
30 </section>
31 <section name="reference_section" title="Reference dataset" expanded="true">
32 <param name="reference" type="data" format="csv,tsv,msp">
33 <label>Reference compound list</label>
34 <help><![CDATA[
35 A list of retention time and retention index pairs.
36 Expected columns for RT (oneof): ['rt', 'retention_time'].
37 Expected columns for RI (oneof): ['carbon_number', 'ri', 'retention_index'].
38 ]]></help>
39 </param>
40 <param name="reference_rt_units" type="select" display="radio" help="Retention time units in the reference file.">
41 <option value="seconds" selected="true">Seconds</option>
42 <option value="min">Minutes</option>
43 </param>
44 </section>
40 <param label="Computation method" name="method" type="select" display="radio" help="Computation method to use."> 45 <param label="Computation method" name="method" type="select" display="radio" help="Computation method to use.">
41 <option value="kovats" selected="true">Kovats</option> 46 <option value="kovats" selected="true">Kovats</option>
42 <!-- <option value="cubicspline">CubicSpline </option> --> 47 <option value="cubicspline">CubicSpline </option>
43 </param> 48 </param>
44 </inputs> 49 </inputs>
45 50
46 <outputs> 51 <outputs>
47 <data label="RI using $method of ${query.element_identifier}" name="output" format_source="query" /> 52 <data label="RI using $method of ${query_section.query.element_identifier}" name="output" format_source="query" metadata_source="query"/>
48 </outputs> 53 </outputs>
49 54
50 <tests> 55 <tests>
51 <test> 56 <test>
52 <param name="query" value="aplcms_aligned_peaks.csv" ftype="csv" /> 57 <param name="query" value="aplcms_aligned_peaks.csv" ftype="csv" />
58 <param name="query_rt_units" value="seconds" />
53 <param name="reference" value="Alkanes_20210325.csv" ftype="csv" /> 59 <param name="reference" value="Alkanes_20210325.csv" ftype="csv" />
60 <param name="reference_rt_units" value="seconds" />
54 <param name="method" value="kovats" /> 61 <param name="method" value="kovats" />
55 <output name="output" file="results.csv" ftype="csv"/> 62 <output name="output" file="results.csv" ftype="csv"/>
56 </test> 63 </test>
57 </tests> 64 </tests>
58 65