Mercurial > repos > iuc > megan_daa_meganizer

changeset 1:f1b6527ba952 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 374a2824a264468316f04281ed211079015503b5"
author iuc
date Tue, 07 Dec 2021 10:17:41 +0000
parents ca7c839a75ab
children bb2a8bd85c85
files daa_meganizer.xml macros.xml
diffstat 2 files changed, 22 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/daa_meganizer.xml	Fri Dec 03 23:10:15 2021 +0000
+++ b/daa_meganizer.xml	Tue Dec 07 10:17:41 2021 +0000
@@ -47,7 +47,7 @@
 && mv '$input_identifier' '$output'
     ]]></command>
     <inputs>
-        <param argument="--in" type="data" format="daa" label="Input DAA file"/>
+        <expand macro="input_daa_param"/>
         <section name="advanced_options" title="Advanced options" expanded="false">
             <param argument="--metaDataFile" type="data" format="tabular" multiple="true" optional="true" label="Files containing metadata to be included in the output files"/>
             <expand macro="long_reads_param"/>
@@ -58,9 +58,7 @@
             <expand macro="read_assignment_mode_param"/>
             <expand macro="con_file_param"/>
             <expand macro="mapdb_param"/>
-            <param argument="--only" type="text" value="" label="Names of classifications to use" help="Leave blank to use all classifications">
-                <expand macro="sanitize_query" validinitial="string.ascii_letters,string.punctuation"/>
-            </param>
+            <expand macro="only_named_classifications_param"/>
         </section>
     </inputs>
     <outputs>
--- a/macros.xml	Fri Dec 03 23:10:15 2021 +0000
+++ b/macros.xml	Tue Dec 07 10:17:41 2021 +0000
@@ -38,9 +38,28 @@
             </when>
         </conditional>
     </macro>
+    <macro name="input_daa_param">
+        <param argument="--in" type="data" format="daa" label="Input DAA file"/>
+    </macro>
     <macro name="long_reads_param">
         <param argument="--longReads" type="boolean" truevalue="--longReads" falsevalue="" checked="false" label="Parse and analyse input reads as long reads?"/>
     </macro>
+    <macro name="max_matches_per_read_param">
+        <param argument="--maxMatchesPerRead" type="integer" value="100" label="Maximum matches per read"/>
+    </macro>
+    <macro name="only_named_classifications_param">
+        <param argument="--only" type="text" value="" label="Names of classifications to use" help="Leave blank to use all classifications">
+            <sanitizer>
+                <valid initial="@VALIDINITIAL@">
+                    <remove value="&apos;" />
+                    <add value="|" />
+                </valid>
+                <mapping initial="none">
+                    <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
+                </mapping>
+            </sanitizer>
+        </param>
+    </macro>
     <macro name="classification_options">
         <option value="EC" selected="true">EC</option>
         <option value="EGGNOG">EGGNOG</option>
@@ -102,7 +121,7 @@
             <mapping initial="none">
                 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
             </mapping>
-       </sanitizer>
+        </sanitizer>
     </xml>
     <xml name="citations">
         <citations>