Mercurial > repos > iuc > raceid_filtnormconf

comparison raceid_filtnormconf.xml @ 8:c891d8b33ede draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 455bad7eca54164f95755174904842907846bb42"
author iuc
date Mon, 20 Dec 2021 10:12:14 +0000
parents d45f092caf24
children 8b917923f7d4
comparison
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7:d45f092caf24 8:c891d8b33ede
1 <tool id="raceid_filtnormconf" name="Initial processing using RaceID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" > 1 <tool id="raceid_filtnormconf" name="Initial processing using RaceID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>performs filtering, normalisation, and confounder removal to generate a normalised and filtered count matrix of single-cell RNA data</description> 2 <description>performs filtering, normalisation, and confounder removal to generate a normalised and filtered count matrix of single-cell RNA data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <import>macros_cheetah.xml</import> 5 <import>macros_cheetah.xml</import>
6 </macros> 6 </macros>
54 </section> 54 </section>
55 </inputs> 55 </inputs>
56 <outputs> 56 <outputs>
57 <data name="outtable" format="tabular" label="${tool.name} on ${on_string}: Normalised Matrix" /> 57 <data name="outtable" format="tabular" label="${tool.name} on ${on_string}: Normalised Matrix" />
58 <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" /> 58 <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" />
59 <data name="outrdat" format="rdata" label="${tool.name} on ${on_string}: RDS" /> 59 <data name="outrdat" format="rds" label="${tool.name} on ${on_string}: RDS" />
60 <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Metrics" /> 60 <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Metrics" />
61 </outputs> 61 </outputs>
62 <tests> 62 <tests>
63 <test expect_num_outputs="4"> 63 <test expect_num_outputs="4">
64 <!-- This is a file with a single word 'test', which prompts the scripts to use the test intestinalData in the library --> 64 <!-- This is a file with a single word 'test', which prompts the scripts to use the test intestinalData in the library -->
79 <section name="filt" > 79 <section name="filt" >
80 <param name="mintotal" value="1050" /> 80 <param name="mintotal" value="1050" />
81 <param name="minexpr" value="1" /> 81 <param name="minexpr" value="1" />
82 <param name="minnumber" value="3" /> 82 <param name="minnumber" value="3" />
83 </section> 83 </section>
84 <output name="outrdat" value="matrix.filter.rdat" compare="sim_size" delta="1000" /> 84 <output name="outrdat" value="matrix.filter.rdat" compare="sim_size" />
85 <output name="outpdf" value="matrix.filter.pdf" compare="sim_size" delta="10" /> 85 <output name="outpdf" value="matrix.filter.pdf" compare="sim_size" delta="10" />
86 </test> 86 </test>
87 <test expect_num_outputs="4"> 87 <test expect_num_outputs="4">
88 <!-- defaults, but manually specified. No opts, no CC. Generates identical to above --> 88 <!-- defaults, but manually specified. No opts, no CC. Generates identical to above -->
89 <param name="intable" value="use.intestinal" /> 89 <param name="intable" value="use.intestinal" />