diff macros.xml @ 11:65be0674bb70 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"

--- a/macros.xml	Fri May 17 10:03:56 2019 -0400
+++ b/macros.xml	Wed Sep 09 20:06:18 2020 +0000
@@ -1,11 +1,21 @@
 <?xml version='1.0' encoding='UTF-8'?>
+<!-- CTD2Galaxy depends on this file and on the stdio, advanced_options macros!
+     You can edit this file to add your own macros, if you so desire, or you can
+     add additional macro files using the m/macros parameter -->
 <macros>
+  <token name="@TOOL_VERSION@">2.5</token>
+  <token name="@GALAXY_VERSION@">0</token>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="2.3">openms</requirement>
-      <requirement type="package" version="15.12.15.2">xtandem</requirement>
-      <requirement type="package" version="1.0">fido</requirement>
-      <requirement type="package" version="2017.07.21">msgf_plus</requirement>
+      <requirement type="package" version="@TOOL_VERSION@">openms</requirement>
+      <requirement type="package" version="@TOOL_VERSION@">openms-thirdparty</requirement>
+      <!-- makeblastdb for OMSSAAdapter -->
+      <requirement type="package" version="2.9.0">blast</requirement>
+      <requirement type="package" version="8.0.192">openjdk</requirement>
+      <!--<requirement type="package" version="5.0.0">tpp</requirement>-->
+      <!-- for realpath (used e.g. in LuciphorAdapter) -->
+	  <!--<requirement type="package" version="8.25">coreutils</requirement>-->
+	  <requirement type="package" version="1.4">ctdopts</requirement>
       <yield/>
     </requirements>
   </xml>
@@ -21,8 +31,8 @@
       <citation type="doi">doi:10.1186/1471-2105-9-163</citation>
     </citations>
   </xml>
-  <xml name="advanced_options">
-    <conditional name="adv_opts">
+  <xml name="adv_opts_macro">
+    <conditional name="adv_opts_cond">
       <param name="adv_opts_selector" type="select" label="Advanced Options">
         <option value="basic" selected="True">Hide Advanced Options</option>
         <option value="advanced">Show Advanced Options</option>
@@ -33,4 +43,87 @@
       </when>
     </conditional>
   </xml>
-</macros>
+
+  <!-- sanitizers and validators -->
+  <xml name="list_string_val">
+    <validator type="regex" message="parameter must not start with $">^[^$]</validator>
+    
+    <validator type="regex" message="a space separated list of string is needed (strings that contain spaces can be quoted with &quot;)">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator>
+  </xml>
+  <xml name="list_string_san">
+    <sanitizer>
+      <valid initial="string.printable">
+<!--        <remove value="'"/>-->
+<!--        <remove value="\"/>--><!-- otherwise the user could quote the final quote -->
+<!--        <remove value="`"/>-->
+<!--        <remove value="$"/>-->
+<!--        <remove value="&lt;"/>-->
+	<!--<remove value="&amp;"/> removed for MascotAdapterOnline -Mascot_server:export_params which is a URL POST string which can contain & .. could be mapped to &amp; but there is still a & -->
+        <!--<remove value=";"/>-->
+<!--        <remove value="#"/>-->
+      </valid>
+    </sanitizer>
+  </xml>
+  <xml name="list_float_valsan">
+    <validator type="regex" message="a space separated list of float values is required">^ *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?( *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)* *$</validator>
+    <yield/>
+    <sanitizer>
+      <valid initial="string.digits">
+        <add value=" "/>
+        <add value="."/>
+        <add value="E"/>
+        <add value="e"/>
+        <add value="+"/>
+        <add value="-"/>
+      </valid>
+    </sanitizer>
+  </xml>
+  <xml name="list_integer_valsan">
+    <validator type="regex" message="a space separated list of integer values is required">^ *[+-]?[0-9]+( *[+-]?[0-9]+)* *$</validator>
+    <yield/>
+    <sanitizer>
+      <valid initial="string.digits">
+        <add value=" "/>
+        <add value="+"/>
+        <add value="-"/>
+      </valid>
+    </sanitizer>
+  </xml>
+
+  <!-- helper function to quote space separated strings -->
+  <token name="@QUOTE_FOO@">
+#def quote(s):
+    #set $s = [ _ for _ in $s.split(" ") if _ != "" ]
+    #set $q = False
+    #for $i, $p in enumerate($s):
+        #if $p == "":
+            #continue
+        #end if
+        #if $p.startswith('"'):
+            #set $q = True
+        #end if
+##        #if p.startswith('-'):
+##            #set p = "\\" + p
+##        #elif p.startswith('"-'):
+##            #set p = "\\" + p[1:]
+##        #end if
+        #if not $q:
+            #set $s[i] = '"%s"' % p
+        #end if
+        #if $p.endswith('"'):
+            #set $q = False
+        #end if
+    #end for
+    #return " ".join($s)
+#end def
+  </token>
+
+<token name="@EXT_FOO@"><![CDATA[#def oms2gxyext(o)
+    #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'}
+    #return m[o]
+#end def
+#def gxy2omsext(g)
+    #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'}
+    #return m[g]
+#end def
+]]></token></macros>