# HG changeset patch
# User wolma
# Date 1513586309 18000
# Node ID e76e813f615ac42367397b793faabd5a647edc36
# Parent  d801b0675eb5ff32dd6e6fa95860c9ce3002475d
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 24cc567ad105450d1c554f09a3467eff671d9864

diff -r d801b0675eb5 -r e76e813f615a macros.xml
--- a/macros.xml	Sat Nov 11 18:18:54 2017 -0500
+++ b/macros.xml	Mon Dec 18 03:38:29 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>
 
 
diff -r d801b0675eb5 -r e76e813f615a snap_caller.xml
--- a/snap_caller.xml	Sat Nov 11 18:18:54 2017 -0500
+++ b/snap_caller.xml	Mon Dec 18 03:38:29 2017 -0500
@@ -165,7 +165,9 @@
                 help="Corresponds to the second value of the SNAP option -s."/>
                 <param name="discard_overlapping_mates" type="text" optional="true"
                 label="discard overlapping read pairs of type"
-                help="Consider overlapping mate pairs of the given orientation type(s) anomalous and discard them; allowed values: RF, FR, FF, RR; multiple types may be specified as a comma-separated list and ALL can be used as a shortcut for discarding all overlapping mate pairs; leave blank to retain all overlapping pairs." />
+                help="Consider overlapping mate pairs of the given orientation type(s) anomalous and discard them; allowed values: RF, FR, FF, RR; multiple types may be specified as a comma-separated list and ALL can be used as a shortcut for discarding all overlapping mate pairs; leave blank to retain all overlapping pairs.">
+                    <validator type="expression" message="only RF, FR, FF, RR or ALL are allowed as input">not value or all(token.strip(' ') in ['RF', 'FR', 'FF', 'RR', 'ALL'] for token in value.split(','))</validator>
+                </param>
                 <param name="maxdist" type="integer" value="8" 
                 label="edit distance (default: 8)" 
                 help="maximum edit distance allowed per read or pair (SNAP option -d); higher values allow more divergent alignments to be found, but increase the rate of misalignments."/>
@@ -329,7 +331,9 @@
 	                    help="Corresponds to the second value of the SNAP option -s."/>
 	                    <param name="discard_overlapping_mates" type="text" optional="true" value=""
 	                    label="discard overlapping read pairs of type" 
-	                    help="Consider overlapping mate pairs of the given orientation type(s) anomalous and discard them; allowed values: RF, FR, FF, RR; multiple types may be specified as a comma-separated list and ALL can be used as a shortcut for discarding all overlapping mate pairs; leave blank to retain all overlapping pairs." />
+	                    help="Consider overlapping mate pairs of the given orientation type(s) anomalous and discard them; allowed values: RF, FR, FF, RR; multiple types may be specified as a comma-separated list and ALL can be used as a shortcut for discarding all overlapping mate pairs; leave blank to retain all overlapping pairs.">
+	                        <validator type="expression" message="only RF, FR, FF, RR or ALL are allowed as input">not value or all(token.strip(' ') in ['RF', 'FR', 'FF', 'RR', 'ALL'] for token in value.split(','))</validator>
+                        </param>
             	        <param name="maxdist" type="integer" optional="true" value="0"
             	        label="edit distance"
             	        help="maximum edit distance allowed per read or pair (SNAP option -d); higher values allow more divergent alignments to be found, but increase the rate of misalignments."/>