diff hicHyperoptDetectLoops.xml @ 0:dde6b320a34b draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicHyperoptDetectLoops.xml	Tue Mar 16 20:14:14 2021 +0000
@@ -0,0 +1,78 @@
+<tool id="hicexplorer_hichyperoptDetectLoops" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description>optimizes parameters for hicDetectLoops</description>
+    <macros>
+        <token name="@BINARY@">hicHyperoptDetectLoops</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
+        @BINARY@
+
+            --matrix  'matrix.$matrix_h5_cooler.ext'
+
+            #if '$proteinFile':
+                --proteinFile '$proteinFile'
+            #end if
+
+            #if '$maximumNumberOfLoops':
+                --maximumNumberOfLoops '$maximumNumberOfLoops'
+            #end if
+
+            #if '$resolution':
+                --resolution '$resolution'
+            #end if
+
+            #if '$runs':
+                --runs '$runs'
+            #end if
+
+            --outputFileName hyperopt_result.txt
+
+            --threads @THREADS@
+]]>
+    </command>
+    <inputs>
+        <expand macro="matrix_h5_cooler_macro" />
+        <param argument="--proteinFile" type='data' format="bed" label="Protein peak file in bed format" help= "The protein file to validate the detected loops." />
+        <param argument="--maximumNumberOfLoops" type="integer" min='0' max='100000' label="Maximum number of loops" help= "The maximum number of loops that should be used for optimization computation." value='10000' />
+        <param argument="--resolution" type="integer" min='0' max='100000000' label="Resolution of the matrix" help="The matrix resolution of the Hi-C interaction matrix." value='10000' />
+        <param argument="--runs" type="integer" min='2' max='10000' label="Hyperopt runs" help= "The number of iterations hyperopt uses to search for a result" value='100' />
+    </inputs>
+    <outputs>
+        <data name='hyperopt_result' from_work_dir='hyperopt_result.txt' format='txt' label='Computed parameters for hicDetectLoops' />
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
+            <param name="proteinFile" value="hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak" />
+            <param name="maximumNumberOfLoops" value="5" />
+            <param name="resolution" value="2" />
+            <param name="runs" value="5" />
+            <output name="hyperopt_result" file="hicHyperoptDetectLoops/loops.bedgraph" ftype="txt" compare="sim_size" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Hyperopt parameter optimization loop detection
+==============================================
+
+Compute with a protein peak data file (bed format) optimal parameters for the loop calling. Useful proteins are e.g. CTCF or cohesin.
+
+_________________
+
+Usage
+-----
+
+A command line example is available below (easily matchable in Galaxy using each field information):
+
+̀`$ hicHyperoptDetectLoops -m matrix.cool -o hyperopt_result.txt --maximumNumberOfLoops 10000 --resolution 10000 --runs 100`
+
+
+For more information about HiCExplorer please consider our documentation on readthedocs.io_.
+
+.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
+
+]]>    </help>
+    <expand macro="citations" />
+</tool>