diff hicFindRestrictionSites.xml @ 0:8339f6708553 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicFindRestrictionSites.xml	Mon Dec 16 15:36:09 2019 -0500
@@ -0,0 +1,54 @@
+<tool id="hicexplorer_hicfindrestrictionsites" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>identify TAD boundaries by computing the degree of separation of each Hi-C matrix bin</description>
+    <macros>
+        <token name="@BINARY@">findRestSite</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        @BINARY@
+            --fasta '$fasta'
+            --searchPattern '$searchPattern'
+            --outFile restriction_site.bed
+
+    ]]></command>
+    <inputs>
+        <param argument="--fasta" type="data" format='fasta'
+                        label="Fasta file for the organism genome."
+                        help="The organism genome fasta file to compute the restriction enzyme position."/>
+        <param argument="--searchPattern" type="text" value=""
+                label="Restriction enzyme sequence"
+                help='Search pattern. For example, for HindIII this pattern is \"AAGCTT\". 
+                    Both, forward and reverse strand are searched for a match. The pattern 
+                    is a regexp and can contain regexp specif syntax 
+                    (see https://docs.python.org/2/library/re.html). For example the pattern
+                    CG..GC will find all occurrence of CG followed by any two bases and then GC.'/>       
+    </inputs>
+    <outputs>
+
+        <data name="restrictionSites" from_work_dir="restriction_site.bed" format="bed" label="${tool.name} on ${fasta.name} ${searchPattern} [${on_string}]: Restriction sites"/>
+    
+    </outputs>
+    <tests>
+        <test>
+            <param name="fasta" value="hicFindRestrictionSites/reference_genome.fasta"/>
+
+            <param name="searchPattern" value="GTAC"/>
+            
+            <output name="restrictionSites" file="hicFindRestrictionSites/restriction_sites.bed" ftype="bed" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Find restriction sites
+======================
+
+This scripts find the locations of a given restriction enzyme sequence. This file can be used to build an Hi-C interaction matrix with restriction enzyme resolution by hicBuildMatrix.
+
+
+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>