<tool id="client_38" name="genesbygenetype    ">
  <description> Client for method: genesbygenetype , Web service: http://eupathdb.org/eupathdb/webservices/GeneQuestions/GenesByGeneType.wadl </description>
  <command interpreter="python">
  	client_1.py
	#if $cond_source.optional_param_source=="no":
  	$output
	$servicetype
      $url
        $method
     http://eupathdb.org/webservices/GeneQuestions
	organism
	 #if $source0.source0_source=="user":
	 $source0.user_param0
	 #else:
	 fileInput
	 $source0.cached_param0
	 #end if
	includePseudogenes
	 #if $source1.source1_source=="user":
	 $source1.user_param1
	 #else:
	 fileInput
	 $source1.cached_param1
	 #end if
	geneType
	 #if $source2.source2_source=="user":
	 $source2.user_param2
	 #else:
	 fileInput
	 $source2.cached_param2
	 #end if
   	#else:
  	$output
	$servicetype
    $url
    $method
http://eupathdb.org/webservices/GeneQuestions
	organism
	 #if $source0.source0_source=="user":
	 $source0.user_param0
	 #else:
	 fileInput
	 $source0.cached_param0
	 #end if
	includePseudogenes
	 #if $source1.source1_source=="user":
	 $source1.user_param1
	 #else:
	 fileInput
	 $source1.cached_param1
	 #end if
	geneType
	 #if $source2.source2_source=="user":
	 $source2.user_param2
	 #else:
	 fileInput
	 $source2.cached_param2
	 #end if
	o-fields
	 #if $cond_source.source3.source3_source=="user":
	 $cond_source.source3.user_param3
	 #else:
	 fileInput
	 $cond_source.source3.cached_param3
	 #end if
	o-tables
	 #if $cond_source.source4.source4_source=="user":
	 $cond_source.source4.user_param4
	 #else:
	 fileInput
	 $cond_source.source4.cached_param4
	 #end if
   	#end if
</command>
  <inputs>
     <param name="servicetype" type="hidden" value="REST"/>
     <param name="url" type="hidden" value="http://eupathdb.org/eupathdb/webservices/GeneQuestions/GenesByGeneType.wadl" />
     <param name="method" type="hidden" value="http://eupathdb.org/webservices/GeneQuestions" />
<conditional name="source0">
    <param name="source0_source" type="select" label="Organism Source"> 
      <option value="cached" selected="true">Param value will be taken from previous step</option> 
      <option value="user">User will enter the param value</option> 
    </param>
    <when value="user">
    <param name="user_param0" type="select" label="Select Organism" help="see tip below">
      <option value="Entamoeba**dispar" >Entamoeba dispar</option>
       <option value="Entamoeba**histolytica" >Entamoeba histolytica</option>
       <option value="Entamoeba**invadens" >Entamoeba invadens</option>
       <option value="Cryptosporidium**parvum" >Cryptosporidium parvum</option>
       <option value="Cryptosporidium**hominis" >Cryptosporidium hominis</option>
       <option value="Cryptosporidium**muris" >Cryptosporidium muris</option>
       <option value="Giardia**Assemblage**A**isolate**WB" >Giardia Assemblage A isolate WB</option>
       <option value="Giardia**Assemblage**B**isolate**GS" >Giardia Assemblage B isolate GS</option>
       <option value="Giardia**Assemblage**E**isolate**P15" >Giardia Assemblage E isolate P15</option>
       <option value="Encephalitozoon**cuniculi" >Encephalitozoon cuniculi</option>
       <option value="Encephalitozoon**intestinalis" >Encephalitozoon intestinalis</option>
       <option value="Enterocytozoon**bieneusi" >Enterocytozoon bieneusi</option>
       <option value="Babesia**bovis" >Babesia bovis</option>
       <option value="Theileria**annulata" >Theileria annulata</option>
       <option value="Theileria**parva" >Theileria parva</option>
       <option value="Plasmodium**falciparum" >Plasmodium falciparum</option>
       <option value="Plasmodium**vivax" >Plasmodium vivax</option>
       <option value="Plasmodium**yoelii" >Plasmodium yoelii</option>
       <option value="Plasmodium**berghei" >Plasmodium berghei</option>
       <option value="Plasmodium**chabaudi" >Plasmodium chabaudi</option>
       <option value="Plasmodium**knowlesi" >Plasmodium knowlesi</option>
       <option value="Toxoplasma**gondii" >Toxoplasma gondii</option>
       <option value="Neospora**caninum" >Neospora caninum</option>
       <option value="Trichomonas**vaginalis" >Trichomonas vaginalis</option>
       <option value="Trypanosoma**cruzi" >Trypanosoma cruzi</option>
       <option value="Leishmania**braziliensis" >Leishmania braziliensis</option>
       <option value="Leishmania**infantum" >Leishmania infantum</option>
       <option value="Leishmania**major" >Leishmania major</option>
       <option value="Leishmania**mexicana" >Leishmania mexicana</option>
       <option value="Trypanosoma**brucei" >Trypanosoma brucei</option>
       <option value="Trypanosoma**congolense" >Trypanosoma congolense</option>
       <option value="Trypanosoma**vivax" >Trypanosoma vivax</option>
     </param> 
 </when>
 <when value="cached">
    <param name = "cached_param0" type="data" label="Choose the step from which to get the parameter Organism"/> 
 </when></conditional><conditional name="source1">
    <param name="source1_source" type="select" label="Include Pseudogenes Source"> 
      <option value="cached" selected="true">Param value will be taken from previous step</option> 
      <option value="user">User will enter the param value</option> 
    </param>
    <when value="user">
    <param name="user_param1" type="select" label="Select Include Pseudogenes" help="see tip below">
      <option value="No" selected="true">No</option>
       <option value="Yes" >Yes</option>
       <option value="Pseudogenes**Only" >Pseudogenes Only</option>
     </param> 
 </when>
 <when value="cached">
    <param name = "cached_param1" type="data" label="Choose the step from which to get the parameter Include Pseudogenes"/> 
 </when></conditional><conditional name="source2">
    <param name="source2_source" type="select" label="Gene type Source"> 
      <option value="cached" selected="true">Param value will be taken from previous step</option> 
      <option value="user">User will enter the param value</option> 
    </param>
    <when value="user">
    <param name="user_param2" type="select" label="Select Gene type" help="see tip below">
      <option value="protein**coding" selected="true">protein coding</option>
       <option value="snRNA**encoding" >snRNA encoding</option>
       <option value="tRNA**encoding" >tRNA encoding</option>
       <option value="rRNA**encoding" >rRNA encoding</option>
       <option value="misc**RNA" >misc RNA</option>
       <option value="snoRNA**encoding" >snoRNA encoding</option>
       <option value="SRP**RNA**encoding" >SRP RNA encoding</option>
       <option value="RNase**P**RNA" >RNase P RNA</option>
       <option value="RNase**MRP**RNA" >RNase MRP RNA</option>
       <option value="repeat**region" >repeat region</option>
       <option value="scRNA**encoding" >scRNA encoding</option>
     </param> 
 </when>
 <when value="cached">
    <param name = "cached_param2" type="data" label="Choose the step from which to get the parameter Gene type"/> 
 </when></conditional>  <conditional name="cond_source">
  <param name="optional_param_source" type="select" label="Display Additional Parameters"> 
 <option value="no" selected="true">no</option> 
 <option value="yes">yes</option> 
 </param> 
    <when value="no"> 
     </when>
    <when value="yes"> 

<conditional name="source3">
  <param name="source3_source" type="select" label="Output Fields Source"> 
    <option value="cached" selected="true">Param value will be taken from previous step</option> 
 <option value="user">User will enter the param value</option> 
</param>
         <when value="user"><param name="user_param3" type="select" label="Select Output Fields" help="see tip below">
 <option value="all" >all</option>
  <option value="none" selected="true">none</option>
  <option value="primary_key" >primary_key</option>
  <option value="formatted_gene_id" >formatted_gene_id</option>
  <option value="sequence_id" >sequence_id</option>
  <option value="chromosome" >chromosome</option>
  <option value="chromosome_order_num" >chromosome_order_num</option>
  <option value="location_text" >location_text</option>
  <option value="strand" >strand</option>
  <option value="gene_type" >gene_type</option>
  <option value="exon_count" >exon_count</option>
  <option value="transcript_length" >transcript_length</option>
  <option value="cds_length" >cds_length</option>
  <option value="product" >product</option>
  <option value="protein_length" >protein_length</option>
  <option value="tm_count" >tm_count</option>
  <option value="molecular_weight" >molecular_weight</option>
  <option value="isoelectric_point" >isoelectric_point</option>
  <option value="ec_numbers_string" >ec_numbers_string</option>
  <option value="ortholog_number" >ortholog_number</option>
  <option value="paralog_number" >paralog_number</option>
  <option value="orthomcl_name" >orthomcl_name</option>
  <option value="signalp_scores" >signalp_scores</option>
  <option value="signalp_peptide" >signalp_peptide</option>
  <option value="ann_go_function" >ann_go_function</option>
  <option value="ann_go_process" >ann_go_process</option>
  <option value="ann_go_component" >ann_go_component</option>
  <option value="pred_go_function" >pred_go_function</option>
  <option value="pred_go_process" >pred_go_process</option>
  <option value="pred_go_component" >pred_go_component</option>
  <option value="organism" >organism</option>
  <option value="is_pseudo" >is_pseudo</option>
  <option value="protein_sequence" >protein_sequence</option>
  <option value="transcript_sequence" >transcript_sequence</option>
  <option value="cds" >cds</option>
  <option value="wdk_weight" >wdk_weight</option>
     </param> 
 </when>
<when value="cached">
 <param name = "cached_param3" type="data" label="Choose the step from which to get the parameter Output Fields"/> 
  </when></conditional>

<conditional name="source4">
  <param name="source4_source" type="select" label="Output Tables Source"> 
    <option value="cached" selected="true">Param value will be taken from previous step</option> 
 <option value="user">User will enter the param value</option> 
</param>
         <when value="user"><param name="user_param4" type="select" label="Select Output Tables" help="see tip below">
 <option value="all" >all</option>
  <option value="none" selected="true">none</option>
  <option value="SNPs" >SNPs</option>
  <option value="GeneModelDump" >GeneModelDump</option>
  <option value="InterPro" >InterPro</option>
  <option value="TMHMM" >TMHMM</option>
  <option value="LowComplexity" >LowComplexity</option>
  <option value="SignalP" >SignalP</option>
  <option value="BlastP" >BlastP</option>
  <option value="Genbank" >Genbank</option>
  <option value="SageTags" >SageTags</option>
  <option value="Notes" >Notes</option>
  <option value="UserComments" >UserComments</option>
  <option value="CommunityExpComments" >CommunityExpComments</option>
  <option value="EcNumber" >EcNumber</option>
  <option value="MassSpec" >MassSpec</option>
  <option value="GoTerms" >GoTerms</option>
  <option value="Phenotype" >Phenotype</option>
  <option value="Y2hInteractions" >Y2hInteractions</option>
  <option value="Orthologs" >Orthologs</option>
  <option value="MetabolicPathways" >MetabolicPathways</option>
  <option value="TaskComments" >TaskComments</option>
  <option value="ArrayElements" >ArrayElements</option>
  <option value="TwoChannelDiffExpr" >TwoChannelDiffExpr</option>
  <option value="ProteinExpression" >ProteinExpression</option>
  <option value="Mr4Reagents" >Mr4Reagents</option>
  <option value="ProteinDatabase" >ProteinDatabase</option>
  <option value="GeneLinkouts" >GeneLinkouts</option>
  <option value="3dPreds" >3dPreds</option>
  <option value="PdbSimilarities" >PdbSimilarities</option>
  <option value="Epitopes" >Epitopes</option>
  <option value="IsolateOverlap" >IsolateOverlap</option>
     </param> 
 </when>
<when value="cached">
 <param name = "cached_param4" type="data" label="Choose the step from which to get the parameter Output Tables"/> 
  </when></conditional>
 </when>
 </conditional>
</inputs>
  <outputs>
    <data format="tabular" name="output" />
  </outputs>
  <help>
Replace white space with ** in all parameter values

.. class:: infomark

**TIP:** Organism type is xsd:string

.. class:: infomark

**TIP:** Include Pseudogenes type is xsd:string

.. class:: infomark

**TIP:** Gene type type is xsd:string
  </help>
</tool>