Mercurial > repos > guerler > springsuite
comparison spring_mcc.xml @ 41:f316caf098a6 draft default tip
"planemo upload commit 685e1236afde7cf6bb0c9236de06998d2c211dd3"
| author | guerler |
|---|---|
| date | Mon, 01 Mar 2021 15:02:36 +0000 |
| parents | 172398348efd |
| children |
comparison
equal
deleted
inserted
replaced
| 40:06337927c198 | 41:f316caf098a6 |
|---|---|
| 1 <tool id="spring_mcc" name="SPRING MCC" version="0.1.0" python_template_version="3.5" license="MIT"> | 1 <tool id="spring_mcc" name="SPRING MCC" version="0.1.0" python_template_version="3.5" license="MIT"> |
| 2 <description>plot generator</description> | 2 <description>plot generator</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="3.3.2">matplotlib</requirement> | 4 <requirement type="package" version="3.3.2">matplotlib</requirement> |
| 5 <requirement type="package" version="1.2.0">pandas</requirement> | |
| 5 </requirements> | 6 </requirements> |
| 6 <command detect_errors="exit_code"><![CDATA[ | 7 <command detect_errors="exit_code"><![CDATA[ |
| 7 python3 '$__tool_directory__/spring_mcc.py' -i '$input' -b '$database' -m '$method' -l '$sampling.locations' -ra '$sampling.regiona' -rb '$sampling.regionb' -n '$sampling.negative' -o '$output' | 8 python3 '$__tool_directory__/spring_mcc.py' -i '$input' -b '$database' -e '$experiment' -l '$sampling.locations' -ra '$sampling.regiona' -rb '$sampling.regionb' -n '$sampling.negative' -o '$output' |
| 8 ]]></command> | 9 ]]></command> |
| 9 <inputs> | 10 <inputs> |
| 11 <param name="experiment" type="text" label="Title" help="Experiment title" value="Results"/> | |
| 10 <param name="input" type="data" format="tabular" label="Interacting Pairs" help="Prediction input containing UniProt Accession codes (2-columns)."/> | 12 <param name="input" type="data" format="tabular" label="Interacting Pairs" help="Prediction input containing UniProt Accession codes (2-columns)."/> |
| 11 <conditional name="sampling"> | 13 <conditional name="sampling"> |
| 12 <param name="type" type="select" label="Non-interacting Pairs" display="radio" help="Specify how to determine non-interacting pairs."> | 14 <param name="type" type="select" label="Non-interacting Pairs" display="radio" help="Specify how to determine non-interacting pairs."> |
| 13 <option value="random">Random Sampling</option> | 15 <option value="random">Random Sampling</option> |
| 14 <option value="uniprot">Sampling with UniProt Localization</option> | 16 <option value="uniprot">Sampling with UniProt Localization</option> |
| 48 <param name="regiona" type="hidden" value="" /> | 50 <param name="regiona" type="hidden" value="" /> |
| 49 <param name="regionb" type="hidden" value="" /> | 51 <param name="regionb" type="hidden" value="" /> |
| 50 </when> | 52 </when> |
| 51 </conditional> | 53 </conditional> |
| 52 <param name="database" type="data" format="tabular" label="BioGRID Database" help="BioGRID Database in TAB 3.0 format."/> | 54 <param name="database" type="data" format="tabular" label="BioGRID Database" help="BioGRID Database in TAB 3.0 format."/> |
| 53 <param name="method" type="select" label="Experimental Method" help="Choose a specific experimental method name."> | |
| 54 <option value="Affinity Capture-MS">Affinity Capture-MS</option> | |
| 55 <option value="Biochemical Activity">Biochemical Activity</option> | |
| 56 <option value="Co-crystal Structure">Co-crystal Structure</option> | |
| 57 <option value="Co-fractionation">Co-fractionation</option> | |
| 58 <option value="Co-localization">Co-localization</option> | |
| 59 <option value="Co-purification">Co-purification</option> | |
| 60 <option value="Far Western">Far Western</option> | |
| 61 <option value="FRET">FRET</option> | |
| 62 <option value="PCA">PCA</option> | |
| 63 <option value="Reconstituted Complex">Reconstituted Complex</option> | |
| 64 <option value="Two-hybrid">Two-hybrid</option> | |
| 65 </param> | |
| 66 </inputs> | 55 </inputs> |
| 67 <outputs> | 56 <outputs> |
| 68 <data format="png" name="output" label="SPRING MCC Image" /> | 57 <data format="png" name="output" label="SPRING MCC Image" /> |
| 69 </outputs> | 58 </outputs> |
| 70 <tests> | 59 <tests> |
| 71 <test> | 60 <test> |
| 72 <param name="input" value="mcc/human_hv1h2.txt" /> | 61 <param name="input" value="mcc/human_hv1h2.txt" /> |
| 73 <param name="database" value="mcc/biogrid_fret.txt" /> | 62 <param name="database" value="mcc/biogrid_fret.txt" /> |
| 74 <param name="method" value="FRET" /> | |
| 75 <output name="output" file="mcc/human_hv1h2.png" /> | 63 <output name="output" file="mcc/human_hv1h2.png" /> |
| 76 </test> | 64 </test> |
| 77 </tests> | 65 </tests> |
| 78 <help><![CDATA[ | 66 <help><![CDATA[ |
| 79 This tool generates a MCC plot for a given 2-column tabular prediction file containing UniProt Accession codes. The prediction is compared | 67 This tool generates a MCC plot for a given 2-column tabular prediction file containing UniProt Accession codes. The prediction is compared |