Mercurial > repos > azomics > autospill
comparison autospill.xml @ 1:7f5bf24d5aeb draft
"planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/autospill commit 8fafcaef24d23a785759004c5794a9cae485dfb1"
| author | azomics |
|---|---|
| date | Sat, 19 Jun 2021 10:57:45 +0000 |
| parents | 315be37a7ac9 |
| children | 3293c160f73c |
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| 0:315be37a7ac9 | 1:7f5bf24d5aeb |
|---|---|
| 1 <tool id="autospill" name="Autospill" version="0.1.0+galaxy0" profile="19.01" python_template_version="3.5"> | 1 <tool id="autospill" name="Autospill" version="0.2.0+galaxy0" profile="19.01" python_template_version="3.5"> |
| 2 <description> | 2 <description> |
| 3 calculates spillover coefficients with robust linear models and then refines spillover coefficients iteratively | 3 calculates spillover coefficients with robust linear models and then refines spillover coefficients iteratively |
| 4 </description> | 4 </description> |
| 5 <requirements> | 5 <requirements> |
| 6 <requirement type="package" version="0.1.0">r-autospill</requirement> | 6 <requirement type="package" version="0.2.0">r-autospill</requirement> |
| 7 </requirements> | 7 </requirements> |
| 8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
| 9 mkdir input_dir; | 9 mkdir input_dir; |
| 10 #for $fcs in $fcs_list: | 10 #for $fcs in $fcs_list: |
| 11 ln -s '$fcs' input_dir/'$fcs.element_identifier'; | 11 ln -s '$fcs' input_dir/'$fcs.element_identifier'; |
| 203 <!-- | 203 <!-- |
| 204 <collection name="compensation_plots" label="${tool.name} compensation plots on ${on_string}"> | 204 <collection name="compensation_plots" label="${tool.name} compensation plots on ${on_string}"> |
| 205 <discover_datasets pattern="__designation_and_ext__" format="png" directory="figure_compensation" visible="true" /> | 205 <discover_datasets pattern="__designation_and_ext__" format="png" directory="figure_compensation" visible="true" /> |
| 206 </collection> --> | 206 </collection> --> |
| 207 </outputs> | 207 </outputs> |
| 208 <tests> | |
| 209 <test> | |
| 210 <param name="fcs_list" value="Compensation Controls_FITC Stained Control_001.fcs,Compensation Controls_PE-CF594 Stained Control_025.fcs,Compensation Controls_PE-Cy5.5 Stained Control_027.fcs"/> | |
| 211 <param name="fcs_metadata" value="fcs_control.csv" ftype="csv"/> | |
| 212 <param name="get_figure_scatter" value="false"/> | |
| 213 <param name="get_error" value="false"/> | |
| 214 <param name="get_gates" value="false"/> | |
| 215 <output name="spillover_matrix"> | |
| 216 <assert_contents> | |
| 217 <has_n_lines n="4" /> | |
| 218 </assert_contents> | |
| 219 </output> | |
| 220 </test> | |
| 221 </tests> | |
| 208 <help><![CDATA[ | 222 <help><![CDATA[ |
| 209 Autospill: a principled framework that simplifies the analysis of multichromatic flow cytometry data | 223 Autospill: a principled framework that simplifies the analysis of multichromatic flow cytometry data |
| 210 ---------------------------------------------------------------------------------------------------- | 224 ---------------------------------------------------------------------------------------------------- |
| 211 | 225 |
| 212 Calculates spillover coefficients with robust linear models and then refines spillover coefficients iteratively. | 226 Calculates spillover coefficients with robust linear models and then refines spillover coefficients iteratively. |