Mercurial > repos > iuc > schicexplorer_schicadjustmatrix

comparison scHicAdjustMatrix.xml @ 2:edc219b0f5e1 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d
author iuc
date Fri, 14 Apr 2023 14:17:14 +0000
parents 3c45c9f30143
children
comparison
equal deleted inserted replaced
1:3c45c9f30143 2:edc219b0f5e1
1 <tool id="schicexplorer_schicadjustmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="schicexplorer_schicadjustmatrix" name="@BINARY@" version="@TOOL_VERSION@.1" profile="@PROFILE@">
2 <description>clusters single-cell Hi-C interaction matrices on the raw data</description> 2 <description>clusters single-cell Hi-C interaction matrices on the raw data</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">scHicAdjustMatrix</token> 4 <token name="@BINARY@">scHicAdjustMatrix</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 @BINARY@ 9 @BINARY@
10 10
11 --matrix '$matrix_scooler' 11 --matrix "$matrix_scooler"
12 --action $action_selector 12 --action $action_selector
13 #if $chromosomes: 13 #if $chromosomes:
14 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ]) 14 #set $chromosome = " ".join([ "\"%s\"" % $chrom for $chrom in str($chromosomes).split(" ") ])
15 --chromosomes $chromosome 15 --chromosomes $chromosome
16 #end if 16 #end if
17 17
18 18
19 --outFileName adjusted_matrix.scool 19 --outFileName adjusted_matrix.scool
20 20
21 --threads @THREADS@ 21 --threads @THREADS@
22
23
24
25 ]]></command> 22 ]]></command>
26 <inputs> 23 <inputs>
27 24
28 <expand macro="matrix_scooler_macro"/> 25 <expand macro="matrix_scooler_macro"/>
29 <param name="action_selector" type="select" label="Action to take apply on matrices:"> 26 <param name="action_selector" type="select" label="Action to take apply on matrices:">
30 <option value="keep" selected="True">Keep the listed chromosomes</option> 27 <option value="keep" selected="true">Keep the listed chromosomes</option>
31 <option value="remove" >Remove the listed chromosomes</option> 28 <option value="remove" >Remove the listed chromosomes</option>
32 </param> 29 </param>
33 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/> 30 <param name="chromosomes" type="text" label="List of chromosomes to consider" help="Please separate the chromosomes by space"/>
34 </inputs> 31 </inputs>
35 <outputs> 32 <outputs>
36 <data name="outFileName" from_work_dir="adjusted_matrix.scool" format="scool" label="${tool.name} on ${on_string}: Adjusted matrix"/> 33 <data name="outFileName" from_work_dir="adjusted_matrix.scool" format="scool" label="${tool.name} on ${on_string}: Adjusted matrix"/>
37 </outputs> 34 </outputs>
38 <tests> 35 <tests>
39 <test> 36 <test>
40 <param name='matrix_scooler' value='test_matrix.scool' /> 37 <param name="matrix_scooler" value="test_matrix.scool" />
41 <param name='clusterMethod_selector' value='keep' /> 38 <param name="action_selector" value="keep" />
42 <param name='chromosomes' value='chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chrX' /> 39 <param name="chromosomes" value="chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chrX" />
43 <output name="outFileName" ftype="scool"> 40 <output name="outFileName" ftype="scool">
44 <assert_contents> 41 <assert_contents>
45 <has_h5_keys keys='Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins, 42 <has_h5_keys keys="Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins,
46 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/end, 43 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/end,
47 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/start, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms, 44 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/start, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms,
48 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/length, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/name, 45 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/length, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/name,
49 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/indexes, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/indexes/bin1_offset, 46 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/indexes, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/indexes/bin1_offset,
50 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/indexes/chrom_offset, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/pixels, 47 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/indexes/chrom_offset, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/pixels,
188 Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/bins/start, Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/chroms, 185 Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/bins/start, Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/chroms,
189 Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/chroms/length, Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/chroms/name, 186 Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/chroms/length, Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/chroms/name,
190 Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/indexes, Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/indexes/bin1_offset, 187 Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/indexes, Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/indexes/bin1_offset,
191 Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/indexes/chrom_offset, Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/pixels, 188 Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/indexes/chrom_offset, Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/pixels,
192 Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/pixels/bin1_id, Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/pixels/bin2_id, 189 Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/pixels/bin1_id, Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/pixels/bin2_id,
193 Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/pixels/count'/> 190 Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/pixels/count"/>
194 </assert_contents> 191 </assert_contents>
195 </output> 192 </output>
196 </test> 193 </test>
197 194
198 </tests> 195 </tests>