view scHicInfo.xml @ 0:35c211c5146d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"

<tool id="schicexplorer_schicinfo" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>information about a single-cell mcool matrix</description>
    <macros>
        <token name="@BINARY@">scHicInfo</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
    #import re
        #set mcoolFile = @ESCAPE_IDENTIFIER_MCOOL@
        ln -s '$matrix_mcooler' '$mcoolFile' &&
        @BINARY@
        --matrix $mcoolFile
        >> matrices_info.txt
    ]]></command>
    <inputs>
        <expand macro="matrix_mcooler_macro"/>
   </inputs>
    <outputs>
        <data name="outFileName" from_work_dir="matrices_info.txt" format="txt" label="${tool.name} on ${on_string}: Matrix Info"/>
    </outputs>
    <tests>
        <test>
            <param name='matrix_mcooler' value='test_matrix.mcool' />
            <output name="outFileName" file="scHicInfo/matrices_info.txt" ftype="txt" compare="sim_size" delta="4000"/>
        </test>
    </tests>
    <help><![CDATA[

Consensus matrices
==================

scHicInfo gives information about the single-cell Hi-C mcool file. For example: 

.. code-block::

    Filename: nagano2017_raw.mcool
    Contains 3882 single-cell matrices
    The information stored via cooler.info of the first cell is:

    bin-size 1000000
    bin-type fixed
    creation-date 2019-05-16T11:46:31.826214
    format HDF5::Cooler
    format-url https://github.com/mirnylab/cooler
    format-version 3
    generated-by cooler-0.8.3
    genome-assembly unknown
    metadata {}
    nbins 2744
    nchroms 35
    nnz 55498
    storage-mode symmetric-upper
    sum 486056

For more information about scHiCExplorer please consider our documentation on readthedocs.io_

.. _readthedocs.io: http://schicexplorer.readthedocs.io/
]]></help>
    <expand macro="citations" />

</tool>