| Next changeset 1:c702620c22b1 (2023-04-03) |
|
Commit message:
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" |
|
added:
macros.xml riassigner.xml |
| b |
| diff -r 000000000000 -r f6bf8f1f3224 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Mar 22 16:10:46 2022 +0000 |
| [ |
| @@ -0,0 +1,25 @@ +<macros> + <token name="@TOOL_VERSION@">0.3.2</token> + <xml name="creator"> + <creator> + <person + givenName="Helge" + familyName="Hecht" + url="https://github.com/hechth" + identifier="0000-0001-6744-996X" /> + <organization + url="https://www.recetox.muni.cz/" + email="GalaxyToolsDevelopmentandDeployment@space.muni.cz" + name="RECETOX MUNI" /> + </creator> + </xml> + + <token name="@HELP@"> + <![CDATA[ + RIAssigner can be used to read data from .msp, .csv and .tsv files using matchms and pandas and to compute the + retention indices for the data. A reference list of retention indexed compounds (traditionally an Alkane series) + with retention times is used to compute the RI for a query dataset of retention time values using the van den + Dool method or by using cubic spline based interpolation. + ]]> + </token> +</macros> |
| b |
| diff -r 000000000000 -r f6bf8f1f3224 riassigner.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/riassigner.xml Tue Mar 22 16:10:46 2022 +0000 |
| [ |
| @@ -0,0 +1,74 @@ +<tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy1" profile="19.05"> + <description>compute retention indices</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="creator"/> + + <requirements> + <requirement type="package" version="@TOOL_VERSION@">riassigner</requirement> + </requirements> + + <command detect_errors="exit_code"><![CDATA[ + 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}" && + cp -r 'output.${query_section.query.ext}' '${output}' + ]]> + </command> + + <inputs> + <section name="query_section" title="Query dataset" expanded="true"> + <param name="query" type="data" format="csv,tsv,msp"> + <label>Query compound list</label> + <help><![CDATA[ + A list of compounds with retention times for which to compute the retention index. + Expected columns for RT (oneof): ['rt', 'retention_time']. + ]]></help> + </param> + <param name="query_rt_units" type="select" display="radio" help="Retention time units in the query file."> + <option value="seconds" selected="true">Seconds</option> + <option value="min">Minutes</option> + </param> + </section> + <section name="reference_section" title="Reference dataset" expanded="true"> + <param name="reference" type="data" format="csv,tsv,msp"> + <label>Reference compound list</label> + <help><![CDATA[ + A list of retention time and retention index pairs. + Expected columns for RT (oneof): ['rt', 'retention_time']. + Expected columns for RI (oneof): ['carbon_number', 'ri', 'retention_index']. + ]]></help> + </param> + <param name="reference_rt_units" type="select" display="radio" + help="Retention time units in the reference file."> + <option value="seconds" selected="true">Seconds</option> + <option value="min">Minutes</option> + </param> + </section> + <param label="Computation method" name="method" type="select" display="radio" help="Computation method to use."> + <option value="kovats" selected="true">Kovats</option> + <option value="cubicspline">CubicSpline</option> + </param> + </inputs> + + <outputs> + <data label="RI using $method of ${query_section.query.element_identifier}" name="output" format_source="query" + metadata_source="query"/> + </outputs> + + <tests> + <test> + <param name="query" value="aplcms_aligned_peaks.csv" ftype="csv"/> + <param name="query_rt_units" value="seconds"/> + <param name="reference" value="Alkanes_20210325.csv" ftype="csv"/> + <param name="reference_rt_units" value="seconds"/> + <param name="method" value="kovats"/> + <output name="output" file="results.csv" ftype="csv"/> + </test> + </tests> + + <help> + <![CDATA[ + @HELP@ + ]]> + </help> +</tool> |