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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
author iuc
date Tue, 18 Apr 2023 13:18:07 +0000
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1 <tool id="episcanpy_build_matrix" name="Build count matrix" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>with EpiScanpy</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements"/>
8 <expand macro="version_command"/>
9 <command detect_errors="exit_code"><![CDATA[
10 bgzip -c '$fragment_file' > fragments.gz &&
11 tabix -p bed fragments.gz &&
12 cat '$script_file' > '$hidden_output' &&
13 python '$script_file' >> '$hidden_output' &&
14 touch 'anndata_info.txt' &&
15 cat 'anndata_info.txt' @CMD_prettify_stdout@
16 ]]></command>
17 <configfiles>
18 <configfile name="script_file"><![CDATA[
19 @CMD_imports@
20 peaks = esc.ct.load_peaks('$peaks_file')
21 esc.ct.norm_peaks(peaks, extension=$extension)
22 esc.ct.bld_mtx_bed(
23 fragment_file='fragments.gz',
24 feature_region=peaks,
25 #if $reference_chr.chr_select == 'custom'
26 #set $chromosomes = ([x.strip() for x in str($reference_chr.chromosomes).split(',')])
27 chromosomes=$chromosomes,
28 #else
29 chromosomes='$reference_chr.chr_select',
30 #end if
31 save='anndata.h5ad')
32 ]]></configfile>
33 </configfiles>
34 <inputs>
35 <param name="fragment_file" type="data" format="bed" label="ATAC fragments file" />
36 <param name="peaks_file" type="data" format="tabular" label="Features file" help="Peaks BED file or MACS2 narrowPeak file"/>
37 <param name="extension" type="integer" value="0" min="0" label="Number of bases to extend both sides of peaks" />
38 <conditional name="reference_chr">
39 <param name="chr_select" type="select" label="Select the chromosomes of the species you are considering" >
40 <option value="human">Human chromosomes ['1', '2', '3', ... , '22', 'X', 'Y']</option>
41 <option value="mouse">Mouse chromosomes ['1', '2', '3', ... ', '19', 'X', 'Y']</option>
42 <option value="custom">Custom list of chromosomes</option>
43 </param>
44 <when value="human" />
45 <when value="mouse" />
46 <when value="custom">
47 <param name="chromosomes" value="" type="text" label="Enter comma seperated list of chromosome ids (without chr prefix)" >
48 <expand macro="sanitize_query" />
49 </param>
50 </when>
51 </conditional>
52 <expand macro="inputs_common_advanced"/>
53 </inputs>
54 <outputs>
55 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} on ${on_string}: Annotated data matrix"/>
56 <data name="hidden_output" format="txt" label="Log file" hidden="true" >
57 <filter>advanced_common['show_log']</filter>
58 </data>
59 </outputs>
60 <tests>
61 <test expect_num_outputs="2">
62 <!-- count matrix -->
63 <param name="fragment_file" value="chrY.fragments.bed" />
64 <param name="peaks_file" value="chrY.peaks.bed" />
65 <conditional name="reference_chr">
66 <param name="chr_select" value="custom" />
67 <param name="chromosomes" value="Y" />
68 </conditional>
69 <section name="advanced_common">
70 <param name="show_log" value="true" />
71 </section>
72 <output name="anndata_out" file="chrY.h5ad" ftype="h5ad" compare="sim_size"/>
73 </test>
74 </tests>
75 <help>
76 .. class:: infomark
77
78 **What it does**
79
80 Builds single-cell ATAC-seq count matrix in Anndata format.
81
82 -----
83
84 **Inputs**
85
86 - ATAC fragments containing the positions of Tn5 integration sites, the cell barcode that the DNA fragment originated from, and the number of times the fragment was sequenced. An example::
87
88 chrY 2650256 2650533 GACCAATGTCCGTAGC 1
89 chrY 2650420 2650463 TGACAACGTACTTCAG 1
90 chrY 2650444 2650643 GTGGATTGTACAAGCG 3
91 chrY 2650639 2650990 ATAGGCTAGGGCTCTC 2
92 chrY 2650650 2650692 GACTAACAGCAACGGT 1
93 chrY 2650699 2650942 TCAAAGCTCAAAGTAG 1
94 chrY 2650768 2650809 TTGTTGTAGGGCATTG 2
95 chrY 2650841 2650873 TTGTTGTAGGGCATTG 1
96 chrY 2650957 2650995 GACTAACAGCAACGGT 1
97 chrY 2651205 2651265 TCAAAGCTCAAAGTAG 1
98 chrY 2651215 2651268 TCACAAGGTCAAGACG 1
99
100 - Features file. A plain BED file with peak locations or narrowPeak file from MACS2.
101
102 **Output**
103
104 - Count matrix in Anndata format.
105
106 </help>
107 <expand macro="citations"/>
108 </tool>