Mercurial > repos > iuc > raceid_filtnormconf

comparison raceid_filtnormconf.xml @ 3:d55e29ac02e3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit d94b3b8a4c7cf8c604279eb1eea24d32b3868922
author iuc
date Mon, 15 Apr 2019 17:55:17 -0400
parents 01290f30211f
children 5d5b14dbd092
comparison
equal deleted inserted replaced
2:56a093c2a3f9 3:d55e29ac02e3
1 <tool id="raceid_filtnormconf" name="Filtering, Normalisation, and Confounder Removal using RaceID" version="@VERSION_RACEID@.@VERSION_PACKAGE@.2" > 1 <tool id="raceid_filtnormconf" name="Filtering, Normalisation, and Confounder Removal using RaceID" version="@VERSION_RACEID@.@VERSION_PACKAGE@.3" >
2 <description>generates a normalised and filtered count matrix of single-cell RNA data</description> 2 <description>generates 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_cluster.xml</import> 5 <import>macros_cluster.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <version_command><![CDATA[ 8 <version_command><![CDATA[
9 Rscript '$__tool_directory__/scripts/cluster.R' @GET_VERSION@ 9 Rscript '$__tool_directory__/scripts/cluster.R' @GET_VERSION@
10 ]]></version_command> 10 ]]>
11 </version_command>
11 12
12 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
13 #set bin = 'cluster.R' 14 #set bin = 'cluster.R'
14 Rscript '$__tool_directory__/scripts/$bin' '$userconf' 2> '$outlog' > /dev/null 15 Rscript '$__tool_directory__/scripts/$bin' '$userconf' 2> '$outlog' > /dev/null
15 ]]></command> 16 ]]></command>
16
17 <configfiles> 17 <configfiles>
18 <configfile name="userconf" ><![CDATA[ 18 <configfile name="userconf" ><![CDATA[
19 @STRING2VECTOR@ 19 @STRING2VECTOR@
20 20
21 @FILTNORM_CHEETAH@ 21 @FILTNORM_CHEETAH@
26 <param name="intable" type="data" format="tabular" label="Count Matrix" /> 26 <param name="intable" type="data" format="tabular" label="Count Matrix" />
27 <section name="filt" title="Filtering" expanded="true" > 27 <section name="filt" title="Filtering" expanded="true" >
28 <param name="mintotal" type="integer" min="1" value="3000" label="Min Transcripts" help="The minimum total transcripts required. Cells with less than mintotal transcripts are filtered out." /> 28 <param name="mintotal" type="integer" min="1" value="3000" label="Min Transcripts" help="The minimum total transcripts required. Cells with less than mintotal transcripts are filtered out." />
29 <param name="minexpr" type="integer" min="1" value="5" label="Min Expression" help="The minimum required transcript counts of a gene in the minimum number of cells (below)" /> 29 <param name="minexpr" type="integer" min="1" value="5" label="Min Expression" help="The minimum required transcript counts of a gene in the minimum number of cells (below)" />
30 <param name="minnumber" type="integer" min="1" value="5" label="Min Cells" help="The minumum number of cells for gene expression to be counted" /> 30 <param name="minnumber" type="integer" min="1" value="5" label="Min Cells" help="The minumum number of cells for gene expression to be counted" />
31 <param name="hist_geq_one" type="boolean" checked="false" label="Count filtered features greater than or equal to 1" help="By default features are counted if they are above zero, but RaceID adds 0.1 to all counts after normalisation to create a non-zero dataset." />
31 <expand macro="use_defaults_no" > 32 <expand macro="use_defaults_no" >
32 <param name="knn" type="integer" min="0" value="10" label="K-nearest-neighbours" help="Number of nearest neighbors used to infer corresponding cell types in different batches" /> 33 <param name="knn" type="integer" min="0" value="10" label="K-nearest-neighbours" help="Number of nearest neighbors used to infer corresponding cell types in different batches" />
33 <param name="CGenes" type="text" optional="true" label="CGenes" help="Filter out genes with correlated expression for cell type inference" > 34 <param name="CGenes" type="text" optional="true" label="CGenes" help="Filter out genes with correlated expression for cell type inference" >
34 <expand macro="sanitize_string_vector" /> 35 <expand macro="sanitize_string_vector" />
35 </param> 36 </param>
63 <option value="ica">ICA</option> 64 <option value="ica">ICA</option>
64 </param> 65 </param>
65 <param name="logscale" type="boolean" value="false" label="Log-transform data prior to PCA or ICA" help="" /> 66 <param name="logscale" type="boolean" value="false" label="Log-transform data prior to PCA or ICA" help="" />
66 </when> 67 </when>
67 </conditional> 68 </conditional>
68 <param name="use_log" type="boolean" checked="false" label="Output Log?" />
69 </expand> 69 </expand>
70 </section> 70 </section>
71 </inputs> 71 </inputs>
72 <outputs> 72 <outputs>
73 <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" /> 73 <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" />
74 <data name="outrdat" format="rdata" label="${tool.name} on ${on_string}: RDS" /> 74 <data name="outrdat" format="rdata" label="${tool.name} on ${on_string}: RDS" />
75 <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" > 75 <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Metrics" />
76 <filter>use_log</filter>
77 </data>
78 </outputs> 76 </outputs>
79 <tests> 77 <tests>
80 <test> 78 <test expect_num_outputs="3">
81 <!-- This is a file with a single word 'test', which prompts the scripts to use the test intestinalData in the library --> 79 <!-- This is a file with a single word 'test', which prompts the scripts to use the test intestinalData in the library -->
82 <param name="intable" value="use.intestinal" /> 80 <param name="intable" value="use.intestinal" />
83 <output name="outpdf" value="intestinal.filter.pdf" compare="sim_size" delta="50" /> 81 <output name="outpdf" value="intestinal.filter.pdf" compare="sim_size" delta="50" />
82 <output name="outlog" value="intestinal.filter.log" />
84 </test> 83 </test>
85 <test> 84 <test expect_num_outputs="3">
86 <!-- defaults, feeding in a matrix with reduced filtering --> 85 <!-- defaults, feeding in a matrix with reduced filtering -->
87 <param name="intable" value="matrix.tabular" /> 86 <param name="intable" value="matrix.tabular" />
88 <section name="filt" > 87 <section name="filt" >
89 <param name="mintotal" value="1050" /> 88 <param name="mintotal" value="1050" />
90 <param name="minexpr" value="1" /> 89 <param name="minexpr" value="1" />
91 <param name="minnumber" value="3" /> 90 <param name="minnumber" value="3" />
92 </section> 91 </section>
93 <output name="outrdat" value="matrix.filter.rdat" compare="sim_size" delta="300" /> 92 <output name="outrdat" value="matrix.filter.rdat" compare="sim_size" delta="300" />
94 <output name="outpdf" value="matrix.filter.pdf" compare="sim_size" delta="10" /> 93 <output name="outpdf" value="matrix.filter.pdf" compare="sim_size" delta="10" />
95 </test> 94 </test>
96 <test> 95 <test expect_num_outputs="3">
97 <!-- defaults, but manually specified. No opts, no CC. Generates identical to above --> 96 <!-- defaults, but manually specified. No opts, no CC. Generates identical to above -->
98 <param name="intable" value="use.intestinal" /> 97 <param name="intable" value="use.intestinal" />
99 <section name="filt" > 98 <section name="filt" >
100 <param name="mintotal" value="3000" /> 99 <param name="mintotal" value="3000" />
101 <param name="minexpr" value="5" /> 100 <param name="minexpr" value="5" />
106 <param name="bmode" value="RaceID" /> 105 <param name="bmode" value="RaceID" />
107 </expand> 106 </expand>
108 </section> 107 </section>
109 <output name="outpdf" value="intestinal.filter.pdf" compare="sim_size" delta="50" /> 108 <output name="outpdf" value="intestinal.filter.pdf" compare="sim_size" delta="50" />
110 </test> 109 </test>
111 <test> 110 <test expect_num_outputs="3">
111 <!-- defaults, but histogram adjustment -->
112 <param name="intable" value="use.intestinal" />
113 <section name="filt" >
114 <param name="hist_geq_one" value="true" />
115 </section>
116 <output name="outpdf" value="matrix.filter.geqone.pdf" compare="sim_size" delta="10" />
117 </test>
118 <test expect_num_outputs="3">
112 <!-- Advanced. Opts, CC used --> 119 <!-- Advanced. Opts, CC used -->
113 <param name="intable" value="use.intestinal" /> 120 <param name="intable" value="use.intestinal" />
114 <section name="filt" > 121 <section name="filt" >
115 <param name="mintotal" value="2000" /> 122 <param name="mintotal" value="2000" />
116 <param name="minexpr" value="3" /> 123 <param name="minexpr" value="3" />
134 </expand> 141 </expand>
135 </section> 142 </section>
136 <output name="outpdf" value="intestinal_advanced.filter.pdf" compare="sim_size" delta="150" /> 143 <output name="outpdf" value="intestinal_advanced.filter.pdf" compare="sim_size" delta="150" />
137 </test> 144 </test>
138 </tests> 145 </tests>
139 <help><![CDATA[ 146 <help><![CDATA[
140 RaceID3 147 RaceID3
141 ======= 148 =======
142 149
143 RaceID is a clustering algorithm for the identification of cell types from single-cell RNA-sequencing data. It was specifically designed for the detection of rare cells which correspond to outliers in conventional clustering methods. 150 RaceID is a clustering algorithm for the identification of cell types from single-cell RNA-sequencing data. It was specifically designed for the detection of rare cells which correspond to outliers in conventional clustering methods.
144 151
169 * *FGenes* → "Lpca5,Atk2" 176 * *FGenes* → "Lpca5,Atk2"
170 177
171 A PDF report will be generated giving metrics about the library size and number of features as histograms, and additional metrics relating to cell-cycle correction will be produced if that option has been selected. 178 A PDF report will be generated giving metrics about the library size and number of features as histograms, and additional metrics relating to cell-cycle correction will be produced if that option has been selected.
172 179
173 ]]> 180 ]]>
174 </help> 181 </help>
175 <expand macro="citations" /> 182 <expand macro="citations" />
176 </tool> 183 </tool>