diff scHicInfo.xml @ 0:35c211c5146d draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scHicInfo.xml	Thu Jan 23 16:02:54 2020 -0500
@@ -0,0 +1,62 @@
+<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>
\ No newline at end of file