Mercurial > repos > iuc > scater_filter

comparison scater-filter.xml @ 1:b7ea9f09c02f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
author iuc
date Tue, 03 Sep 2019 14:27:39 -0400
parents e6ca62ac65c6
children 7a365ec81b52
comparison
equal deleted inserted replaced
0:e6ca62ac65c6 1:b7ea9f09c02f
13 #if str($filter_type.detection_limit): 13 #if str($filter_type.detection_limit):
14 --detection-limit ${filter_type.detection_limit} 14 --detection-limit ${filter_type.detection_limit}
15 #end if 15 #end if
16 #if str($filter_type.library_size): 16 #if str($filter_type.library_size):
17 --library-size ${filter_type.library_size} 17 --library-size ${filter_type.library_size}
18 #end if
19 #if str($filter_type.expressed_genes):
20 --expressed-genes ${filter_type.expressed_genes}
18 #end if 21 #end if
19 #if str($filter_type.percent_counts_MT): 22 #if str($filter_type.percent_counts_MT):
20 --percent-counts-MT ${filter_type.percent_counts_MT} 23 --percent-counts-MT ${filter_type.percent_counts_MT}
21 #end if 24 #end if
22 #else: 25 #else:
33 <option value="pca">PCA</option> 36 <option value="pca">PCA</option>
34 </param> 37 </param>
35 <when value="manual"> 38 <when value="manual">
36 <param name="detection_limit" argument="--detection-limit" type="float" optional="true" label="Number of reads mapped to a gene for it to be counted as expressed" help="Raising this number will raise the stringency and may lower the number of expressed genes" /> 39 <param name="detection_limit" argument="--detection-limit" type="float" optional="true" label="Number of reads mapped to a gene for it to be counted as expressed" help="Raising this number will raise the stringency and may lower the number of expressed genes" />
37 <param name="library_size" argument="--library-size" type="integer" optional="true" label="Minimum library size (mapped reads) to filter cells on" help="Raising this number will raise the stringency and may lower the number of included cells" /> 40 <param name="library_size" argument="--library-size" type="integer" optional="true" label="Minimum library size (mapped reads) to filter cells on" help="Raising this number will raise the stringency and may lower the number of included cells" />
41 <param name="expressed_genes" argument="--expressed-genes" type="integer" optional="true" label="Minimum number of expressed genes to filter cells on" />
38 <param name="percent_counts_MT" argument="--percent-counts-MT" type="float" optional="true" label="Maximum % of mitochondrial genes expressed per cell" help="Cells that exceed this value will be filtered out" /> 42 <param name="percent_counts_MT" argument="--percent-counts-MT" type="float" optional="true" label="Maximum % of mitochondrial genes expressed per cell" help="Cells that exceed this value will be filtered out" />
39 </when> 43 </when>
40 <when value="pca" /> 44 <when value="pca" />
41 </conditional> 45 </conditional>
42 </inputs> 46 </inputs>
47 <test> 51 <test>
48 <param name="input_loom" value="scater_qcready.loom" ftype="loom" /> 52 <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
49 <param name="filter_type_selector" value="manual" /> 53 <param name="filter_type_selector" value="manual" />
50 <param name="detection_limit" value="4" /> 54 <param name="detection_limit" value="4" />
51 <param name="library_size" value="100000" /> 55 <param name="library_size" value="100000" />
56 <param name="expressed_genes" value="400" />
52 <param name="percent_counts_MT" value="33.0" /> 57 <param name="percent_counts_MT" value="33.0" />
53 <output name="output_loom" file="scater_manual_filtered.loom" compare="sim_size" /> 58 <output name="output_loom" file="scater_manual_filtered.loom" compare="sim_size" />
54 </test> 59 </test>
55 <test> 60 <test>
56 <param name="input_loom" value="scater_qcready.loom" ftype="loom" /> 61 <param name="input_loom" value="scater_qcready.loom" ftype="loom" />