diff repeatmasker.xml @ 11:72aade318318 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker commit c4bf14b461856220df4b4bbdbb4b9bbad1ff8749"

--- a/repeatmasker.xml	Fri Dec 11 22:26:02 2020 +0000
+++ b/repeatmasker.xml	Thu May 20 12:56:42 2021 +0000
@@ -1,11 +1,13 @@
-<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.1.1" profile="17.01">
-  <description>screen DNA sequences for interspersed repeats and low complexity regions</description>
-
-  <requirements>
-    <requirement type="package" version="4.1.1">repeatmasker</requirement>
-  </requirements>
-
-  <command detect_errors="exit_code"><![CDATA[
+<tool id="repeatmasker_wrapper" name="RepeatMasker" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01">
+    <description>screen DNA sequences for interspersed repeats and low complexity regions</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro='xrefs'/>
+    <expand macro='edam_ontology' />
+    <expand macro='requirements' />
+    <version_command>repeatmasker --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
     RM_PATH=\$(which RepeatMasker) &&
     if [ -z "\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\$PATH)" >&2 ; exit 1 ; fi &&
 
@@ -97,12 +99,10 @@
           </param>
           <when value="yes">
             <param name="species_list" type="select" label="Species">
-              <option value="vertebrate">Vertebrate (other than below)</option>
-              <option value="mammal">Mammal (other than below)</option>
-              <option value="human" selected="true">Human</option>
-              <option value="rodent">Rodent</option>
-              <option value="mouse">Mouse</option>
-              <option value="rat">Rat</option>
+              <option value="human" selected="true">Human (Homo sapiens)</option>
+              <option value="rodent">Rodent (Order Rodentia)</option>
+              <option value="mouse">Mouse (Mus musculus)</option>
+              <option value="rattus">Rat (Rattus sp.)</option>
               <option value="danio">Danio (zebra fish)</option>
               <option value="drosophila">Fruit fly (Drosophila melanogaster)</option>
               <option value="elegans">Caenorhabditis elegans (nematode)</option>
@@ -219,6 +219,15 @@
       <output name="output_repeat_catalog" file="small_dfam_up.fasta.cat" lines_diff="2" />
       <output name="output_log" file="small_dfam_up.fasta.log" lines_diff="2"/>
     </test>
+    <test expect_num_outputs="4">
+      <param name="input_fasta" value="small.fasta" ftype="fasta" />
+      <param name="source_type" value="dfam" />
+      <param name="species_list" value="rattus" />
+      <output name="output_masked_genome" file="small_dfam_rattus.fasta.masked" />
+      <output name="output_table" file="small_dfam_rattus.fasta.stats" lines_diff="2" />
+      <output name="output_repeat_catalog" file="small_dfam_rattus.fasta.cat" lines_diff="2" />
+      <output name="output_log" file="small_dfam_rattus.fasta.log" lines_diff="2"/>
+    </test>
   </tests>
   <help><![CDATA[
 RepeatMasker is a program that screens DNA for interspersed repeats and low
@@ -234,13 +243,5 @@
 .. _homepage: http://www.repeatmasker.org/webrepeatmaskerhelp.html
     ]]>
   </help>
-  <citations>
-    <citation type="bibtex">
-      @misc{RepeatMasker,
-        title = {RepeatMasker Open-4.0},
-        howpublished = {\url{http://www.repeatmasker.org}},
-        author = {Smit, AFA and Hubley, R and Green, P.},
-        year = {2013-2015}}
-    </citation>
-  </citations>
+  <expand macro="citations" />
 </tool>