--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Nov 22 04:43:57 2018 -0500
@@ -0,0 +1,148 @@
+<macros>
+    <token name="@GET_VERSION@"><![CDATA[ 2>&1 | head -1 | cut -d' ' -f 2 ]]></token>
+    <token name="@STRING2VECTOR@">
+string2numericvector = function(string){
+    #' Converts a string to a valid vector
+    #'
+    #' e.g. "-1,2:5,2"  evaluates to c(-1,2,3,4,5,2)
+    #'
+    #' @param add string2vector function to safe environment
+    #' @return vector of integers
+    terms = unlist(strsplit(string, split=","))
+    res = lapply(terms, function(x){
+        if (grepl(":",x)){
+            l_r = as.integer(c(unlist(strsplit(x,split=":"))))
+            return(seq(l_r[1],l_r[2]))
+        }
+        return(as.integer(x))
+    })
+    return(c(unlist(res)))
+}
+
+string2textvector = function(string){
+    #' Converts a string to a valid string vector
+    #'
+    #'   e.g. "red,yellow,white" evaluates to c("red","yellow","white")
+    return(unlist(strsplit(string,",")))
+}
+    </token>
+    <token name="@VERSION_RACEID@">3</token>
+    <token name="@VERSION_PACKAGE@">0.2</token>
+    <macro name="requirements" >
+        <requirements>
+            <requirement type="package" version="0.1.1">r-raceid</requirement>
+            <requirement type="package" version="1.6.2">bioconductor-scran</requirement>
+        </requirements>
+    </macro>
+    <macro name="yesno_checkedno" >
+        <option value="yes" >Yes</option>
+        <option value="no" selected="true" >No</option>
+    </macro>
+    <macro name="use_defaults_no" >
+        <conditional name="use" >
+            <param name="def" type="select" label="Use Defaults?" >
+                <option value="yes" selected="true" >Yes</option>
+                <option value="no" >No</option>
+            </param>
+            <when value="yes" />
+            <when value="no" >
+                <yield />
+            </when>
+        </conditional>
+    </macro>
+    <macro name="test_nondef" >
+        <conditional name="use" >
+            <param name="def" value="no" />
+            <yield />
+        </conditional>
+    </macro>
+    <macro name="section_test_nondef" >
+        <section name="@SECTIONNAME@" >
+            <expand macro="test_nondef" >
+                <yield />
+            </expand>
+        </section>
+    </macro>
+    <macro name="citations" >
+        <citations>
+            <citation type="doi">10.1038/nature14966</citation>
+            <citation type="doi">10.1038/nmeth.4662</citation>
+        </citations>
+    </macro>
+    <macro name="select_cells" token_sectionname="@SECTIONNAME@" token_sectiontitle="@SECTIONTITLE@" >
+        <section name="@SECTIONNAME@" title="@SECTIONTITLE@" expanded="true" >
+            <param name="name_set" type="text" optional="true" label="Name of Set" >
+                <!-- Aname, Bname -->
+                <expand macro="sanitize_title" />
+            </param>
+            <conditional name="meth" >
+                <param name="type" type="select" label="Selection method" >
+                    <option value="cln" selected="true">Cluster Numbers</option>
+                    <option value="regex" >Regular Expression</option>
+                    <option value="manual" >Manual Selection</option>
+                </param>
+                <when value="cln" >
+                    <param name="selector" type="text" value="" label="List of clusters" >
+                        <expand macro="sanitize_numeric_vector" />
+                    </param>
+                </when>
+                <when value="regex" >
+                    <param name="selector" type="text" value="" label="Regular Expression to select gene names" >
+                        <expand macro="sanitize_regex" />
+                    </param>
+                </when>
+                <when value="manual" >
+                    <param name="selector" type="text" value="" label="List of genes" >
+                        <expand macro="sanitize_string_vector" />
+                    </param>
+                </when>
+            </conditional>
+        </section>
+    </macro>
+    <!-- Sanitizers -->
+    <macro name="sanitize_title">
+        <sanitizer invalid_char="">
+            <valid initial="string.letters,string.digits" >
+                <add value=" " />
+                <add value="_" />
+            </valid>
+        </sanitizer>
+    </macro>
+    <macro name="sanitize_regex" >
+        <sanitizer invalid_char="">
+            <valid initial="string.letters,string.digits">
+                <add value="!"/>
+                <add value="="/>
+                <add value="-"/>
+                <add value="."/>
+                <add value="*"/>
+                <add value="?"/>
+                <add value="+"/>
+                <add value="\\"/>
+                <add value="_"/>
+                <add value="|"/>
+                <add value="&#91;"/> <!-- left square bracket, e.g subselecting from vec[1] -->
+                <add value="&#93;"/> <!-- right square bracket -->
+                <add value="&#40;"/> <!-- left parenthesis -->
+                <add value="&#41;"/> <!-- right parenthesis -->
+            </valid>
+        </sanitizer>
+    </macro>
+    <macro name="sanitize_numeric_vector" >
+        <sanitizer invalid_char="">
+            <valid initial="string.digits">
+                <add value=","/>
+            </valid>
+        </sanitizer>
+    </macro>
+    <macro name="sanitize_string_vector" >
+        <sanitizer invalid_char="">
+            <valid initial="string.letters,string.digits">
+                <add value=","/>
+                <add value="_"/>
+                <add value="-"/>
+                <add value="."/>
+            </valid>
+        </sanitizer>
+    </macro>
+</macros>