Mercurial > repos > iuc > biotradis
comparison tradis_essentiality.xml @ 2:103bd59b3e33 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 6a29aaead9d6b0f69ef70113df58047877fc6ce5"
| author | iuc |
|---|---|
| date | Wed, 04 Nov 2020 15:32:47 +0000 |
| parents | 58234d95978d |
| children | 8e4a4f240961 |
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| 1:58234d95978d | 2:103bd59b3e33 |
|---|---|
| 2 <description></description> | 2 <description></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> | 7 <command detect_errors="aggressive"> |
| 8 <![CDATA[ | 8 <![CDATA[ |
| 9 ln -s '$input_insert_file' input.csv && | 9 ln -s '$input_insert_file' input.csv && |
| 10 tradis_essentiality.R input.csv | 10 tradis_essentiality.R input.csv |
| 11 ]]> | 11 ]]> |
| 12 </command> | 12 </command> |
| 13 | |
| 14 <inputs> | 13 <inputs> |
| 15 <param name="input_insert_file" type="data" format="csv" label="Gene insertion counts" help="Ourput file of `Bio-TraDis counts to gene insertion data` tool"/> | 14 <param name="input_insert_file" type="data" format="csv" label="Gene insertion counts" help="Ourput file of `Bio-TraDis counts to gene insertion data` tool"/> |
| 16 </inputs> | 15 </inputs> |
| 17 | |
| 18 <outputs> | 16 <outputs> |
| 19 | 17 <data name="ess_genes" format="csv" label="${tool.name} on ${on_string}: Essential genes" from_work_dir="input.csv.essen.csv"/> |
| 20 <data name="ess_genes" format="csv" label="${tool.name} on ${on_string} : Essential genes" from_work_dir="input.csv.essen.csv"/> | 18 <data name="ambig_genes" format="csv" label="${tool.name} on ${on_string}: Unclassified genes" from_work_dir="input.csv.ambig.csv"/> |
| 21 <data name="ambig_genes" format="csv" label="${tool.name} on ${on_string} : Unclassified genes" from_work_dir="input.csv.ambig.csv"/> | 19 <data name="all_genes" format="csv" label="${tool.name} on ${on_string}: All genes" from_work_dir="input.csv.all.csv"/> |
| 22 <data name="all_genes" format="csv" label="${tool.name} on ${on_string} : All genes" from_work_dir="input.csv.all.csv"/> | 20 <data name="qc_results" format="pdf" label="${tool.name} on ${on_string}: QC report" from_work_dir="input.csv.QC_and_changepoint_plots.pdf"/> |
| 23 <data name="qc_results" format="pdf" label="${tool.name} on ${on_string} : QC report" from_work_dir="input.csv.QC_and_changepoint_plots.pdf"/> | |
| 24 </outputs> | 21 </outputs> |
| 25 | |
| 26 <tests> | 22 <tests> |
| 27 <test> | 23 <test> |
| 28 <param name="input_insert_file" ftype="csv" value="test.csv"/> | 24 <param name="input_insert_file" ftype="csv" value="test.csv"/> |
| 29 <output name="ess_genes" file="test.csv.essen.csv" compare="sim_size" delta="200" /> | 25 <output name="ess_genes" file="test.csv.essen.csv" compare="sim_size" delta="200" /> |
| 30 <output name="ambig_genes" file="test.csv.ambig.csv" compare="sim_size" delta="200" /> | 26 <output name="ambig_genes" file="test.csv.ambig.csv" compare="sim_size" delta="200" /> |