--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/AssociatePhenotypes.xml	Wed Mar 25 13:23:29 2015 -0600
@@ -0,0 +1,128 @@
+<?xml version="1.0"?>
+
+<tool id="hgvs_assoc_phenos" name="Associate phenotypes to an HGVS table">
+  <description>based on the medical literature</description>
+  <version_string>echo 1.0.0</version_string>
+  <command interpreter="perl">associate_variant_phenotypes $__tool_data_path__ pheno $input_hgvs_table 
+	## Handle preselected gene list of interest
+	#if $preselectedGenesSource.source == "file":
+		$preselectedGenesSource.file_of_genenames
+	#else:
+		#set $glist = str($preselectedGenesSource.genename_list).replace("__cr____cn__", " or ")
+		"$glist"
+	#end if
+
+	## Handle human literature terms
+	#if $litQuerySource.source == "file":
+		$litQuerySource.file_of_phenotypes 
+	#else:
+		#set $qlist = str($litQuerySource.phenotype_list).replace("__cr____cn__", " or ")
+		"$qlist"
+	#end if
+
+        ## Handle human phenotype ontology query
+	##if $hpQuerySource.source == "file":
+		##$hpQuerySource.file_of_mpterms
+	##else:
+		##set $hplist = str($hpQuerySource.autocomplete_OLS_HP).replace(";", " or ")
+		##"$hplist"
+	##end if
+
+        ## Handle mouse knockout query (Mammalian Phenotype Ontology)
+	#if $mpQuerySource.source == "file":
+		$mpQuerySource.file_of_mpterms
+	#else:
+		#set $mplist = str($mpQuerySource.autocomplete_OLS_MP).replace(";", " or ")
+		"$mplist"
+	#end if
+
+	## Handle gene ontology terms
+	#if $goQuerySource.source == "file":
+		$goQuerySource.file_of_goterms
+        #else:
+	#set $golist = str($goQuerySource.autocomplete_OLS_GO).replace(";", " or ")
+		"$golist"
+	#end if
+  </command>
+
+  <inputs>
+    <param name="outfiles_prefix" type="text" label="Prefix for output file names"/>
+    <param format="achri_annotated_snp_table" name="input_hgvs_table" type="data" label="Basic or functionally annotated HGVS variant table"/>
+    <conditional name="litQuerySource">
+       <param name="source" type="select" label="How would you like to specify the phenotypes of interest?">
+          <option value="list">A list</option>
+          <option value="file">A file</option>
+       </param>
+       <when value="file">
+         <param format="text" name="file_of_phenotypes" type="data" label="Text file with one phenotype per line, from most to least important" help="Phenotypes can have boolean operators to allow word order swaps. e.g. 'Develop and delay' will match both 'delayed development' and 'developmental delay'."/>
+       </when>
+       <when value="list">
+         <param name="phenotype_list" type="text" area="True" label="One phenotype per line, from most to least important" help="Phenotypes can have boolean operators to allow word order swaps. e.g. 'Develop AND delay' will match both 'delayed development' and 'developmental delay'."/>
+       </when>
+    </conditional>
+
+    <conditional name="preselectedGenesSource">
+       <param name="source" type="select" label="How would you like to specify preselected genes of interest?">
+          <option value="list">A list</option>
+          <option value="file">A file</option>
+       </param>
+       <when value="file">
+         <param format="text" name="file_of_genenames" type="data" label="Text file with one upper case gene name per line" help="It is recommended to include gene name synonyms to maximize the chance of reference recovery"/>
+       </when>
+       <when value="list">
+         <param name="genename_list" type="text" area="True" label="One upper case gene name per line, e.g. ADH1" help="It is recommended to include gene name synonyms to maximize the chance of reference recovery"/>
+       </when>
+     </conditional>
+
+    <!--<conditional name="hpQuerySource">
+	<param name="source" type="select" label="How would you like to specify Human Phenotype Ontology terms of interest?">
+		<option value="list">A list</option>
+		<option value="file">A file</option>
+	</param>
+	<when value="file">
+		<param format="text" name="file_of_hpterms" type="data" label="Text file with one Human Phenotype term (text) per line"/>
+	</when>
+        <when value="list">
+		<param name="autocomplete_OLS_HP" type="text" label="Semi-colon separated list of HP terms (with autocomplete)" help="For better search results, do not type punctuation or symbols. For example, if you are looking for 4'-(L-tryptophan), try typing 4 L tryp"/>
+	</when> 
+    </conditional>-->
+
+    <conditional name="mpQuerySource">
+	<param name="source" type="select" label="How would you like to specify Mammalian Phenotype terms of interest?">
+		<option value="list">A list</option>
+		<option value="file">A file</option>
+	</param>
+	<when value="file">
+		<param format="text" name="file_of_mpterms" type="data" label="Text file with one Mammalian Phenotype term (text) per line"/>
+	</when>
+        <when value="list">
+		<param name="autocomplete_OLS_MP" type="text" label="Semi-colon separated list of MP terms (with autocomplete)" help="For better search results, do not type punctuation or symbols. For example, if you are looking for 4'-(L-tryptophan), try typing 4 L tryp"/>
+	</when> 
+    </conditional>
+
+    <conditional name="goQuerySource">
+	<param name="source" type="select" label="How would you like to specify Gene Ontology terms of interest?">
+		<option value="list">A list</option>
+		<option value="file">A file</option>
+	</param>
+	<when value="file">
+		<param format="text" name="file_of_goterms" type="data" label="Text file with one gene ontology term (text) per line"/>
+	</when>
+        <when value="list">
+		<param name="autocomplete_OLS_GO" type="text" label="Semi-colon separated list of GO terms (with autocomplete)" help="For better search results, do not type punctuation or symbols. For example, if you are looking for 4'-(L-tryptophan), try typing 4 L tryp"/>
+	</when> 
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="achri_annotated_snp_table" name="out_hgvs_table" type="data" label="${outfiles_prefix} HGVS all variants table with geno-pheno correlates" from_work_dir="pheno.common.hgvs.txt"/>
+  </outputs>
+
+  <tests>
+  </tests>
+
+  <help>
+  This tools adds columns to an HGVS table that include all of the literature references from OMIM, PubMed, ClinVar, the Human Phenotype 
+  Ontology, the Mouse Knockout Phenotypes, and Gene Ontology that match a given set of clinical phenotype query terms. A combined
+  probability of gene-phenotype association is calculated to help the user rank potentially causative genes for presumed genetic disorders.
+  </help>
+</tool>