Mercurial > repos > ebi-gxa > scanpy_normalise_data
comparison scanpy-normalise-data.xml @ 4:f7322b68cc90 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 16c0036a5c5194a70ef201c0c3f37ae8a0b74fd2
| author | ebi-gxa |
|---|---|
| date | Mon, 28 Oct 2019 09:46:16 -0400 |
| parents | 378ea34bbf2a |
| children | 9e42d8795385 |
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| 3:378ea34bbf2a | 4:f7322b68cc90 |
|---|---|
| 1 <?xml version="1.0" encoding="utf-8"?> | 1 <?xml version="1.0" encoding="utf-8"?> |
| 2 <tool id="scanpy_normalise_data" name="Scanpy NormaliseData" version="@TOOL_VERSION@+galaxy2"> | 2 <tool id="scanpy_normalise_data" name="Scanpy NormaliseData" version="@TOOL_VERSION@+galaxy3"> |
| 3 <description>to make all cells having the same total expression</description> | 3 <description>to make all cells having the same total expression</description> |
| 4 <macros> | 4 <macros> |
| 5 <import>scanpy_macros2.xml</import> | 5 <import>scanpy_macros2.xml</import> |
| 6 </macros> | 6 </macros> |
| 7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
| 23 <param name="scale_factor" argument="--normalize-to" type="float" value="1e4" min="0" | 23 <param name="scale_factor" argument="--normalize-to" type="float" value="1e4" min="0" |
| 24 label="Target number to normalise to" help="Aimed counts per cell after normalisation."/> | 24 label="Target number to normalise to" help="Aimed counts per cell after normalisation."/> |
| 25 <param name="fraction" argument="--fraction" type="float" value="1" min="0" max="1" | 25 <param name="fraction" argument="--fraction" type="float" value="1" min="0" max="1" |
| 26 label="Exclude top expressed genes until the remaining account for no greater than specified fraction of total counts" | 26 label="Exclude top expressed genes until the remaining account for no greater than specified fraction of total counts" |
| 27 help="Only non-excluded genes will sum up the target number."/> | 27 help="Only non-excluded genes will sum up the target number."/> |
| 28 <param name="log_transform" argument="--no-log-transform" type="boolean" truevalue="" falsevalue="--no-log-tranform" checked="True" | 28 <param name="log_transform" argument="--no-log-transform" type="boolean" truevalue="" falsevalue="--no-log-transform" checked="True" |
| 29 label="Apply log transform?" help="If enabled, will apply a log transformation following normalisation."/> | 29 label="Apply log transform?" help="If enabled, will apply a log transformation following normalisation."/> |
| 30 <param name="save_raw" argument="--save-raw" type="boolean" truevalue="yes" falsevalue="no" checked="true" | 30 <param name="save_raw" argument="--save-raw" type="boolean" truevalue="yes" falsevalue="no" checked="true" |
| 31 label="Save normalised data in `.raw`" help="The saved normalised data are log1p transformed."/> | 31 label="Save normalised data in `.raw`" help="The saved normalised data are log1p transformed."/> |
| 32 <expand macro="export_mtx_params"/> | 32 <expand macro="export_mtx_params"/> |
| 33 </inputs> | 33 </inputs> |