Mercurial > repos > iuc > schicexplorer_schicinfo

annotate scHicInfo.xml @ 0:35c211c5146d draft

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 2a80f777c0221752232882c0d43b55f2b1dcd223"
author iuc
date Thu, 23 Jan 2020 16:02:54 -0500
parents
children 09f8be8a6e76
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
1 <tool id="schicexplorer_schicinfo" name="@BINARY@" version="@WRAPPER_VERSION@.0">
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
2 <description>information about a single-cell mcool matrix</description>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
3 <macros>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
4 <token name="@BINARY@">scHicInfo</token>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
5 <import>macros.xml</import>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
6 </macros>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
7 <expand macro="requirements" />
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
9 #import re
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
10 #set mcoolFile = @ESCAPE_IDENTIFIER_MCOOL@
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
11 ln -s '$matrix_mcooler' '$mcoolFile' &&
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
12 @BINARY@
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
13 --matrix $mcoolFile
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
14 >> matrices_info.txt
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
15 ]]></command>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
16 <inputs>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
17 <expand macro="matrix_mcooler_macro"/>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
18 </inputs>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
19 <outputs>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
20 <data name="outFileName" from_work_dir="matrices_info.txt" format="txt" label="${tool.name} on ${on_string}: Matrix Info"/>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
21 </outputs>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
22 <tests>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
23 <test>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
24 <param name='matrix_mcooler' value='test_matrix.mcool' />
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
25 <output name="outFileName" file="scHicInfo/matrices_info.txt" ftype="txt" compare="sim_size" delta="4000"/>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
26 </test>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
27 </tests>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
28 <help><![CDATA[
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
29
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
30 Consensus matrices
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
31 ==================
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
32
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
33 scHicInfo gives information about the single-cell Hi-C mcool file. For example:
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
34
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
35 .. code-block::
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
36
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
37 Filename: nagano2017_raw.mcool
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
38 Contains 3882 single-cell matrices
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
39 The information stored via cooler.info of the first cell is:
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
40
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
41 bin-size 1000000
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
42 bin-type fixed
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
43 creation-date 2019-05-16T11:46:31.826214
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
44 format HDF5::Cooler
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
45 format-url https://github.com/mirnylab/cooler
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
46 format-version 3
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
47 generated-by cooler-0.8.3
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
48 genome-assembly unknown
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
49 metadata {}
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
50 nbins 2744
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
51 nchroms 35
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
52 nnz 55498
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
53 storage-mode symmetric-upper
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
54 sum 486056
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
55
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
56 For more information about scHiCExplorer please consider our documentation on readthedocs.io_
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
57
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
58 .. _readthedocs.io: http://schicexplorer.readthedocs.io/
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
59 ]]></help>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
60 <expand macro="citations" />
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
61
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
62 </tool>