diff hicFindRestrictionSites.xml @ 6:8823a9d45ed0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"

--- a/hicFindRestrictionSites.xml	Fri Dec 11 21:44:35 2020 +0000
+++ b/hicFindRestrictionSites.xml	Tue Mar 16 14:51:57 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicfindrestrictionsites" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_hicfindrestrictionsites" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>identify restriction enzyme sites</description>
     <macros>
         <token name="@BINARY@">hicFindRestSite</token>
@@ -11,31 +11,25 @@
             --searchPattern '$searchPattern'
             --outFile restriction_site.bed
 
-    ]]></command>
+    ]]>    </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\".
+        <param argument="--fasta" type="data" format='fasta,fasta.gz' 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.'/>
+                    CG..GC will find all occurrence of CG followed by any two bases and then GC.'>
+            <validator type="expression" message="Only ASCII characters are allowed.">value.isascii()</validator>
+        </param>
     </inputs>
     <outputs>
-
-        <data name="restrictionSites" from_work_dir="restriction_site.bed" format="bed" label="${tool.name} on ${fasta.name} ${searchPattern} [${on_string}]: Restriction sites"/>
-
+        <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"/>
+            <param name="fasta" value="hicFindRestrictionSites/reference_genome.fasta" />
+            <param name="searchPattern" value="GTAC" />
+            <output name="restrictionSites" file="hicFindRestrictionSites/restriction_sites.bed" ftype="bed" />
         </test>
     </tests>
     <help><![CDATA[
@@ -49,6 +43,6 @@
 For more information about HiCExplorer please consider our documentation on readthedocs.io_
 
 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
-]]></help>
+]]>    </help>
     <expand macro="citations" />
 </tool>