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comparison scanpy-normalise-data.xml @ 6:9e42d8795385 draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003
author ebi-gxa
date Mon, 25 Nov 2019 14:36:21 -0500
parents f7322b68cc90
children 4a6b3778fcc4
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5:1442daff0c7c 6:9e42d8795385
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@+galaxy3"> 2 <tool id="scanpy_normalise_data" name="Scanpy NormaliseData" version="@TOOL_VERSION@+galaxy6">
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-transform" 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>
34 34
35 <outputs> 35 <outputs>
36 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Normalised data"/> 36 <expand macro="output_data_obj" description="Normalised data"/>
37 <expand macro="export_mtx_outputs"/> 37 <expand macro="export_mtx_outputs"/>
38 </outputs> 38 </outputs>
39 39
40 <tests> 40 <tests>
41 <test> 41 <test>