| Next changeset 1:b7713d32248b (2022-02-25) |
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Commit message:
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty" |
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added:
rp2biosensor.xml test-data/rp2-results_dmax-16.csv |
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| diff -r 000000000000 -r eaab33f23abf rp2biosensor.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rp2biosensor.xml Wed Jan 05 16:14:32 2022 +0000 |
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| @@ -0,0 +1,65 @@ +<tool id="rp2biosensor" name="rp2biosensor" version="1.0.1"> + <description>Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output</description> + <requirements> + <requirement type="package" version="1.0.1">rp2biosensor</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python -m rp2biosensor + '$rp2_results' + --opath '$html_file' + ]]></command> + <inputs> + <param name="rp2_results" type="data" format="csv" label="RetroPath2 output"/> + </inputs> + <outputs> + <data name="html_file" format="html" label="${tool.name} - ${rp2_results.name}"/> + </outputs> + <tests> + <test> + <!-- test 1: check if identical outputs are produced --> + <param name="rp2_results" value="rp2-results_dmax-16.csv" /> + <output name="html_file" md5="4abb29e769106e75e68a939764dd2e31"/> + </test> + </tests> + <help><![CDATA[ +rp2biosensor +================ + +Generate HTML outputs to explore Sensing Enabling Metabolic Pathway from RetroPath2 results. + +Input +----- + +Required: + +* **rp2_results**\ : (string) RetroPath2.0 results. + +Output +------ + +* **opath**\ : (string) Output path. Default: biosensor.html. + +* **o_sbol_dir**\ : (string) Output type. This could be either (i) "dir" which means ouput files will outputted into this directory, or (ii) "file" which means that all files will be embedded into a single HTML page. Default: file. + +Project Links +------------------ + +* `GitHub <https://github.com/brsynth/rp2biosensor>`_ + +Version +---------- + +1.0.1 + +Authors +------- + +* **Thomas Duigou** + +License +------- + +* `MIT <https://github.com/brsynth/rp2biosensor/blob/master/LICENSE.md>`_ + + ]]></help> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r eaab33f23abf test-data/rp2-results_dmax-16.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rp2-results_dmax-16.csv Wed Jan 05 16:14:32 2022 +0000 |
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| b'@@ -0,0 +1,365 @@\n+"Initial source","Transformation ID","Reaction SMILES","Substrate SMILES","Substrate InChI","Product SMILES","Product InChI","In Sink","Sink name","Diameter","Rule ID","EC number","Score","Iteration"\n+"[target]","TRS_0_0_15","[H]OO[H]>>O=O.[H]N([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])N([H])[H]","[H]OO[H]","InChI=1S/H2O2/c1-2/h1-2H","[H]N([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])N([H])[H]","InChI=1S/C4H12N2/c5-3-1-2-4-6/h1-6H2","1","[Putrescine]","16","[RR-02-8dc897e99097c96f-16-F]","[1.4.3.10]","0.0","0"\n+"[target]","TRS_0_0_52","[H]OO[H]>>O=O.[H]OC(=O)C([H])(N([H])[H])C([H])([H])C([H])([H])C([H])([H])N([H])[H].[H]O[H]","[H]OO[H]","InChI=1S/H2O2/c1-2/h1-2H","[H]OC(=O)C([H])(N([H])[H])C([H])([H])C([H])([H])C([H])([H])N([H])[H]","InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)","1","[Ornithine]","16","[RR-02-4ca02d3108da6f6c-16-F, RR-02-af76c5b7df680327-16-F]","[1.4.3.3, 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