Mercurial > repos > iuc > schicexplorer_schicinfo

comparison scHicInfo.xml @ 1:09f8be8a6e76 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
author iuc
date Tue, 10 Mar 2020 15:10:08 -0400
parents 35c211c5146d
children 41b415c410e3
comparison
equal deleted inserted replaced
0:35c211c5146d 1:09f8be8a6e76
1 <tool id="schicexplorer_schicinfo" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="schicexplorer_schicinfo" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>information about a single-cell mcool matrix</description> 2 <description>information about a single-cell scool matrix</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">scHicInfo</token> 4 <token name="@BINARY@">scHicInfo</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 #import re
10 #set mcoolFile = @ESCAPE_IDENTIFIER_MCOOL@
11 ln -s '$matrix_mcooler' '$mcoolFile' &&
12 @BINARY@ 9 @BINARY@
13 --matrix $mcoolFile 10 --matrix '$matrix_scooler'
14 >> matrices_info.txt 11 >> matrices_info.txt
15 ]]></command> 12 ]]></command>
16 <inputs> 13 <inputs>
17 <expand macro="matrix_mcooler_macro"/> 14 <expand macro="matrix_scooler_macro"/>
18 </inputs> 15 </inputs>
19 <outputs> 16 <outputs>
20 <data name="outFileName" from_work_dir="matrices_info.txt" format="txt" label="${tool.name} on ${on_string}: Matrix Info"/> 17 <data name="outFileName" from_work_dir="matrices_info.txt" format="txt" label="${tool.name} on ${on_string}: Matrix Info"/>
21 </outputs> 18 </outputs>
22 <tests> 19 <tests>
23 <test> 20 <test>
24 <param name='matrix_mcooler' value='test_matrix.mcool' /> 21 <param name='matrix_scooler' value='test_matrix.scool' />
25 <output name="outFileName" file="scHicInfo/matrices_info.txt" ftype="txt" compare="sim_size" delta="4000"/> 22 <output name="outFileName" file="scHicInfo/matrices_info.txt" ftype="txt" compare="sim_size" delta="4000"/>
26 </test> 23 </test>
27 </tests> 24 </tests>
28 <help><![CDATA[ 25 <help><![CDATA[
29 26
30 Consensus matrices 27 Consensus matrices
31 ================== 28 ==================
32 29
33 scHicInfo gives information about the single-cell Hi-C mcool file. For example: 30 scHicInfo gives information about the provided single-cell Hi-C scool file. For example:
34 31
35 .. code-block:: 32 .. code-block::
36 33
37 Filename: nagano2017_raw.mcool 34 Filename: nagano2017_raw.scool
38 Contains 3882 single-cell matrices 35 Contains 3882 single-cell matrices
39 The information stored via cooler.info of the first cell is: 36 The information stored via cooler.info of the first cell is:
40 37
41 bin-size 1000000 38 bin-size 1000000
42 bin-type fixed 39 bin-type fixed