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<?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>