Mercurial > repos > iuc > schicexplorer_schicinfo

comparison scHicInfo.xml @ 0:35c211c5146d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
author iuc
date Thu, 23 Jan 2020 16:02:54 -0500
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-1:000000000000 0:35c211c5146d
1 <tool id="schicexplorer_schicinfo" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>information about a single-cell mcool matrix</description>
3 <macros>
4 <token name="@BINARY@">scHicInfo</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9 #import re
10 #set mcoolFile = @ESCAPE_IDENTIFIER_MCOOL@
11 ln -s '$matrix_mcooler' '$mcoolFile' &&
12 @BINARY@
13 --matrix $mcoolFile
14 >> matrices_info.txt
15 ]]></command>
16 <inputs>
17 <expand macro="matrix_mcooler_macro"/>
18 </inputs>
19 <outputs>
20 <data name="outFileName" from_work_dir="matrices_info.txt" format="txt" label="${tool.name} on ${on_string}: Matrix Info"/>
21 </outputs>
22 <tests>
23 <test>
24 <param name='matrix_mcooler' value='test_matrix.mcool' />
25 <output name="outFileName" file="scHicInfo/matrices_info.txt" ftype="txt" compare="sim_size" delta="4000"/>
26 </test>
27 </tests>
28 <help><![CDATA[
29
30 Consensus matrices
31 ==================
32
33 scHicInfo gives information about the single-cell Hi-C mcool file. For example:
34
35 .. code-block::
36
37 Filename: nagano2017_raw.mcool
38 Contains 3882 single-cell matrices
39 The information stored via cooler.info of the first cell is:
40
41 bin-size 1000000
42 bin-type fixed
43 creation-date 2019-05-16T11:46:31.826214
44 format HDF5::Cooler
45 format-url https://github.com/mirnylab/cooler
46 format-version 3
47 generated-by cooler-0.8.3
48 genome-assembly unknown
49 metadata {}
50 nbins 2744
51 nchroms 35
52 nnz 55498
53 storage-mode symmetric-upper
54 sum 486056
55
56 For more information about scHiCExplorer please consider our documentation on readthedocs.io_
57
58 .. _readthedocs.io: http://schicexplorer.readthedocs.io/
59 ]]></help>
60 <expand macro="citations" />
61
62 </tool>