# HG changeset patch
# User wolma
# Date 1513586484 18000
# Node ID 99dfde12ee53643f7bfb5e984d6ffe1380a18917
# Parent  01e09a4cacf7069ac8d04d7b2eff373e5876bfda
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 24cc567ad105450d1c554f09a3467eff671d9864

diff -r 01e09a4cacf7 -r 99dfde12ee53 annotate_variants.xml
--- a/annotate_variants.xml	Sat Nov 11 18:20:20 2017 -0500
+++ b/annotate_variants.xml	Mon Dec 18 03:41:24 2017 -0500
@@ -31,7 +31,7 @@
 	    #echo ' '.join(str($snpeff_settings.filter).split(','))
 	  #end if
 	  --ofile '$ofile'
-	  --verbose
+	  --verbose --quiet
     ]]></command>
 
     <inputs>
@@ -62,21 +62,26 @@
                 label="Name of an installed SnpEff genome"
                 help="Your input needs to exactly match the name of an installed SnpEff database.">
                     <validator type="expression" message="A SnpEff genome is required to run this tool.">value.strip()</validator>
+                    <expand macro="lex_sam_header" message="Non-ASCII characters are not valid in SnpEff genome names." />
                 </param>
             </when>
         </conditional>
         <section name="codon_tables" title="Codon Table Configuration" expanded="false">
             <param name="genome_codon_table" type="text"
             label="Genome codon table"
-            help="If this genome uses a non-standard codon table and this fact is not declared in the SnpEff config file, specify the table here. The name you provide must match exactly the name of a codon table known to SnpEff." />
+            help="If this genome uses a non-standard codon table and this fact is not declared in the SnpEff config file, specify the table here. The name you provide must match exactly the name of a codon table known to SnpEff.">
+                <expand macro="lex_sam_header" message="Non-ASCII characters are not valid in codon table names." />
+            </param>
             <repeat name="table_specs" default="0" min="0"
             title="Codon tables to use for specific contigs"
             help="Use if certain contigs in the reference genome use a distinct codon table. A typical example is a mitochondrial genome contained as a contig in the reference genome. Contig/codon table assignments declared here will take precedence over a genome codon table set above.">
                 <param name="contig" type="text" label="contig or chromosome name">
                     <validator type="expression" message="This is a required field for a contig/codon table assignment.">value.strip()</validator>
+                    <expand macro="lex_sam_header" message="Non-ASCII characters are not allowed in contig/chromosome names" />
                 </param>
                 <param name="table" type="text" label="uses codon table">
                     <validator type="expression" message="This is a required field for a contig/codon table assignment.">value.strip()</validator>
+                    <expand macro="lex_sam_header" message="Non-ASCII characters are not valid in codon table names." />
                 </param>
             </repeat>
         </section>
diff -r 01e09a4cacf7 -r 99dfde12ee53 macros.xml
--- a/macros.xml	Sat Nov 11 18:20:20 2017 -0500
+++ b/macros.xml	Mon Dec 18 03:41:24 2017 -0500
@@ -1,7 +1,7 @@
 <macros>
     <token name="@MIMODD_VERSION_REQUIRED@">0.1.8</token>
     <token name="@MIMODD_REAL_VERSION@">0.1.8</token>
-    <token name="@MIMODD_WRAPPER_VERSION@">0.1.8_0</token>
+    <token name="@MIMODD_WRAPPER_VERSION@">0.1.8_1</token>
     <token name="@HELP_FOOTER@"><![CDATA[
 ----
 
@@ -9,7 +9,7 @@
 
    For **additional help** see these resources: 
 
-- The complete `MiModD User Guide <http://mimodd.readthedocs.io/en/v0.1.8/usage_toc.html>`__
+- The complete `MiModD User Guide <http://mimodd.readthedocs.io/en/doc0.1.8/usage_toc.html>`__
 
 - The `MiModD help forum <https://groups.google.com/forum/#!forum/mimodd>`__ reachable also via `email <mailto:mimodd@googlegroups.com>`__
 
@@ -41,6 +41,34 @@
             </citation>
         </citations>
     </xml>
+    <macro name="YYYY-MM-DD_format_validator">
+        <validator type="expression" message="YYYY-MM-DD date format required">not value or (len(value.split('-')) == 3 and all(part.isdigit() and len(part)==expect_len for part, expect_len in zip(value.split('-'), [4,2,2])))</validator>
+    </macro>
+    <macro name="known_sequencing_platform options">
+        <option value="ILLUMINA">ILLUMINA</option>
+        <option value="PACBIO">PACBIO</option>
+        <option value="IONTORRENT">IONTORRENT</option>
+        <option value="ONT">ONT</option>
+        <option value="LS454">LS454</option>
+        <option value="SOLID">SOLID</option>
+        <option value="HELICOS">HELICOS</option>
+        <option value="CAPILLARY">CAPILLARY</option>
+    </macro>
+    <macro name="lex_sam_header" token_message="SAM header data may not contain non-ASCII characters.">
+        <validator type="expression" message="@MESSAGE@">not value or all(ord(c) &lt; 127 for c in value)</validator>
+        <sanitizer invalid_char="">
+            <valid initial="string.printable">
+                <remove preset="string.whitespace" value="&#39;" />
+                <add value=" " />
+            </valid>
+            <mapping initial="none">
+                <add source="&#39;" target="&#39;&quot;&#39;&quot;&#39;" />
+                <add source="&#09;" target="&#32;" />
+                <add source="&#10;" target="&#32;" />
+                <add source="&#13;" target="&#32;" />
+            </mapping>
+        </sanitizer>
+    </macro>
 </macros>