Mercurial > repos > iuc > raceid_filtnormconf

comparison raceid_filtnormconf.xml @ 4:5d5b14dbd092 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
author iuc
date Mon, 12 Aug 2019 12:59:06 -0400
parents d55e29ac02e3
children 7608d5faee41
comparison
equal deleted inserted replaced
3:d55e29ac02e3 4:5d5b14dbd092
1 <tool id="raceid_filtnormconf" name="Filtering, Normalisation, and Confounder Removal using RaceID" version="@VERSION_RACEID@.@VERSION_PACKAGE@.3" > 1 <tool id="raceid_filtnormconf" name="Initial processing using RaceID" version="@VERSION_RACEID@.@VERSION_WRAPPER@" >
2 <description>generates 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_cluster.xml</import> 5 <import>macros_cheetah.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <version_command><![CDATA[ 8 <expand macro="version_command_config" prog="cluster.R" cheetah="FILTNORM_CHEETAH" out="2&#62; '$outlog' &#62; /dev/null" />
9 Rscript '$__tool_directory__/scripts/cluster.R' @GET_VERSION@
10 ]]>
11 </version_command>
12
13 <command detect_errors="exit_code"><![CDATA[
14 #set bin = 'cluster.R'
15 Rscript '$__tool_directory__/scripts/$bin' '$userconf' 2> '$outlog' > /dev/null
16 ]]></command>
17 <configfiles>
18 <configfile name="userconf" ><![CDATA[
19 @STRING2VECTOR@
20
21 @FILTNORM_CHEETAH@
22 ]]>
23 </configfile>
24 </configfiles>
25 <inputs> 9 <inputs>
26 <param name="intable" type="data" format="tabular" label="Count Matrix" /> 10 <param name="intable" type="data" format="tabular" label="Count Matrix" />
27 <section name="filt" title="Filtering" expanded="true" > 11 <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." /> 12 <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)" /> 13 <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)" />
68 </conditional> 52 </conditional>
69 </expand> 53 </expand>
70 </section> 54 </section>
71 </inputs> 55 </inputs>
72 <outputs> 56 <outputs>
57 <data name="outtable" format="tabular" label="${tool.name} on ${on_string}: Normalised Matrix" />
73 <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" /> 58 <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" />
74 <data name="outrdat" format="rdata" label="${tool.name} on ${on_string}: RDS" /> 59 <data name="outrdat" format="rdata" label="${tool.name} on ${on_string}: RDS" />
75 <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Metrics" /> 60 <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Metrics" />
76 </outputs> 61 </outputs>
77 <tests> 62 <tests>
78 <test expect_num_outputs="3"> 63 <test expect_num_outputs="4">
79 <!-- 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 -->
80 <param name="intable" value="use.intestinal" /> 65 <param name="intable" value="use.intestinal" />
81 <output name="outpdf" value="intestinal.filter.pdf" compare="sim_size" delta="50" /> 66 <output name="outpdf" value="intestinal.filter.pdf" compare="sim_size" delta="50" />
82 <output name="outlog" value="intestinal.filter.log" /> 67 <output name="outlog" value="intestinal.filter.log" />
68 <output name="outtable" >
69 <assert_contents>
70 <has_n_columns n="288" />
71 <has_text_matching expression="Amdhd2\s0\.000" />
72 <has_text_matching expression="Ammecr1(\s0\s0)+" />
73 </assert_contents>
74 </output>
83 </test> 75 </test>
84 <test expect_num_outputs="3"> 76 <test expect_num_outputs="4">
85 <!-- defaults, feeding in a matrix with reduced filtering --> 77 <!-- defaults, feeding in a matrix with reduced filtering -->
86 <param name="intable" value="matrix.tabular" /> 78 <param name="intable" value="matrix.tabular" />
87 <section name="filt" > 79 <section name="filt" >
88 <param name="mintotal" value="1050" /> 80 <param name="mintotal" value="1050" />
89 <param name="minexpr" value="1" /> 81 <param name="minexpr" value="1" />
90 <param name="minnumber" value="3" /> 82 <param name="minnumber" value="3" />
91 </section> 83 </section>
92 <output name="outrdat" value="matrix.filter.rdat" compare="sim_size" delta="300" /> 84 <output name="outrdat" value="matrix.filter.rdat" compare="sim_size" delta="300" />
93 <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" />
94 </test> 86 </test>
95 <test expect_num_outputs="3"> 87 <test expect_num_outputs="4">
96 <!-- 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 -->
97 <param name="intable" value="use.intestinal" /> 89 <param name="intable" value="use.intestinal" />
98 <section name="filt" > 90 <section name="filt" >
99 <param name="mintotal" value="3000" /> 91 <param name="mintotal" value="3000" />
100 <param name="minexpr" value="5" /> 92 <param name="minexpr" value="5" />
105 <param name="bmode" value="RaceID" /> 97 <param name="bmode" value="RaceID" />
106 </expand> 98 </expand>
107 </section> 99 </section>
108 <output name="outpdf" value="intestinal.filter.pdf" compare="sim_size" delta="50" /> 100 <output name="outpdf" value="intestinal.filter.pdf" compare="sim_size" delta="50" />
109 </test> 101 </test>
110 <test expect_num_outputs="3"> 102 <test expect_num_outputs="4">
111 <!-- defaults, but histogram adjustment --> 103 <!-- defaults, but histogram adjustment -->
112 <param name="intable" value="use.intestinal" /> 104 <param name="intable" value="use.intestinal" />
113 <section name="filt" > 105 <section name="filt" >
114 <param name="hist_geq_one" value="true" /> 106 <param name="hist_geq_one" value="true" />
115 </section> 107 </section>
116 <output name="outpdf" value="matrix.filter.geqone.pdf" compare="sim_size" delta="10" /> 108 <output name="outpdf" value="matrix.filter.geqone.pdf" compare="sim_size" delta="10" />
117 </test> 109 </test>
118 <test expect_num_outputs="3"> 110 <test expect_num_outputs="4">
119 <!-- Advanced. Opts, CC used --> 111 <!-- Advanced. Opts, CC used -->
120 <param name="intable" value="use.intestinal" /> 112 <param name="intable" value="use.intestinal" />
121 <section name="filt" > 113 <section name="filt" >
122 <param name="mintotal" value="2000" /> 114 <param name="mintotal" value="2000" />
123 <param name="minexpr" value="3" /> 115 <param name="minexpr" value="3" />