<tool id="client_31" name="genesbygenetype      ">
  <description> Client for method: genesbygenetype , Web service: http://eupathdb.org/eupathdb/webservices/GeneQuestions/GenesByGeneType.wadl </description>
  <command interpreter="python">
 #if $cond_source.optional_param_source=="no" #client_1.py $output $service http://eupathdb.org/webservices/GeneQuestions/GenesByGeneType.xml organism $param0 includePseudogenes $param1 geneType $param2 #else #client_1.py $output $service http://eupathdb.org/webservices/GeneQuestions/GenesByGeneType.xml organism $param0 includePseudogenes $param1 geneType $param2 o-fields $cond_source.param3 o-tables $cond_source.param4 #end if 
</command>
  <inputs>
<param name='service' type='hidden' value='REST'/>
<param name="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> 
<param name="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> 
<param name="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> 

 <conditional name="cond_source"> 
 <param name="optional_param_source" type="select" label="Show Additional Parameters">
 <option value="no" selected="true">no</option> 
 <option value="yes">yes</option> 
 </param>
<when value="no"> 
 </when><when value="yes"> 
<param name="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> 
<param name="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>
</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>