Mercurial > repos > guerler > spring_mcc
comparison spring_mcc.xml @ 0:c3e9ffb4c98a draft
"planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
| author | guerler |
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| date | Tue, 23 Mar 2021 13:56:55 +0000 |
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| -1:000000000000 | 0:c3e9ffb4c98a |
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| 1 <tool id="spring_mcc" name="SPRING MCC" license="MIT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> | |
| 2 <description>plot generator</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 spring_mcc.py | |
| 9 -i '$input' | |
| 10 -b '$database' | |
| 11 -e '$experiment' | |
| 12 -l '$sampling.locations' | |
| 13 -ra '$sampling.regiona' | |
| 14 -rb '$sampling.regionb' | |
| 15 -n '$sampling.negative' | |
| 16 -o '$output' | |
| 17 ]]> </command> | |
| 18 <inputs> | |
| 19 <param name="experiment" type="text" label="Title" help="Experiment title" value="Results" /> | |
| 20 <param name="input" type="data" format="tabular" label="Interacting Pairs" help="Prediction input containing UniProt Accession codes (2-columns)." /> | |
| 21 <conditional name="sampling"> | |
| 22 <param name="type" type="select" label="Non-interacting Pairs" display="radio" help="Specify how to determine non-interacting pairs."> | |
| 23 <option value="random">Random Sampling</option> | |
| 24 <option value="uniprot">Sampling with UniProt Localization</option> | |
| 25 <option value="negative">Specify non-interacting pairs</option> | |
| 26 </param> | |
| 27 <when value="uniprot"> | |
| 28 <param name="locations" type="data" format="tabular" label="UniProt Localization Database" help="UniProt tabular export with localization column to sample non-interacting pairs." /> | |
| 29 <param name="negative" type="hidden" value="" /> | |
| 30 <param name="regiona" type="select" label="Choose First Subcellular Location"> | |
| 31 <option value="Cell">Cell</option> | |
| 32 <option value="Cytoplasm">Cytoplasm</option> | |
| 33 <option value="Membrane" selected="True">Membrane</option> | |
| 34 <option value="Mitochondrion" selected="True">Mitochondrion</option> | |
| 35 <option value="Nucleus">Nucleus</option> | |
| 36 <option value="Periplasm">Periplasm</option> | |
| 37 <option value="Secreted">Secreted</option> | |
| 38 </param> | |
| 39 <param name="regionb" type="select" label="Choose Second Subcellular Location"> | |
| 40 <option value="Cell">Cell</option> | |
| 41 <option value="Cytoplasm">Cytoplasm</option> | |
| 42 <option value="Membrane" selected="True">Membrane</option> | |
| 43 <option value="Mitochondrion" selected="True">Mitochondrion</option> | |
| 44 <option value="Nucleus">Nucleus</option> | |
| 45 <option value="Periplasm">Periplasm</option> | |
| 46 <option value="Secreted">Secreted</option> | |
| 47 </param> | |
| 48 </when> | |
| 49 <when value="random"> | |
| 50 <param name="locations" type="hidden" value="" /> | |
| 51 <param name="negative" type="hidden" value="" /> | |
| 52 <param name="regiona" type="hidden" value="" /> | |
| 53 <param name="regionb" type="hidden" value="" /> | |
| 54 </when> | |
| 55 <when value="negative"> | |
| 56 <param name="locations" type="hidden" value="" /> | |
| 57 <param name="negative" type="data" format="tabular" label="Non-interacting Pairs" help="Tabular file containing non-interacting pairs (2-columns)." /> | |
| 58 <param name="regiona" type="hidden" value="" /> | |
| 59 <param name="regionb" type="hidden" value="" /> | |
| 60 </when> | |
| 61 </conditional> | |
| 62 <param name="database" type="data" format="tabular" label="BioGRID Database" help="BioGRID Database in TAB 3.0 format." /> | |
| 63 </inputs> | |
| 64 <outputs> | |
| 65 <data format="png" name="output" label="SPRING MCC Image" /> | |
| 66 </outputs> | |
| 67 <tests> | |
| 68 <test> | |
| 69 <param name="input" value="mcc/human_hv1h2.txt" /> | |
| 70 <param name="database" value="mcc/biogrid_fret.txt" /> | |
| 71 <output name="output" file="mcc/human_hv1h2.png" compare="sim_size" /> | |
| 72 </test> | |
| 73 </tests> | |
| 74 <help><![CDATA[ | |
| 75 | |
| 76 **What it does** | |
| 77 | |
| 78 This tool generates a MCC plot for a given 2-column tabular prediction file containing UniProt Accession codes. The prediction is compared | |
| 79 to a given BioGRID database file in TAB 3.0 format. Non-interacting protein pairs are randomly sampled. | |
| 80 | |
| 81 ]]> </help> | |
| 82 <expand macro="citations" /> | |
| 83 </tool> |