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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author ganjoo
date Tue, 07 Jun 2011 18:00:50 -0400
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<tool id="client_7" name="runclustalW2    ">
  <description> Client for method: runclustalW2 , Web service: http://om.cs.uga.edu/demo/clusatlW2.wadl </description>
  <command interpreter="python">
  #client_1.py 
  $output 
  http://www.ebi.ac.uk/Tools/services/restclustalw2/run
  email
#if $source0.source0_source=="user" $source0.user_param0 #else $source0.cached_param0 #end if
#if $cond_source.optional_param_source=="yes"  type
#if $cond_source.source1.source1_source=="user" $cond_source.source1.user_param1 #else $cond_source.source1.cached_param1 #end if
  title
#if $cond_source.source2.source2_source=="user" $cond_source.source2.user_param2 #else $cond_source.source2.cached_param2 #end if
  output
#if $cond_source.source3.source3_source=="user" $cond_source.source3.user_param3 #else $cond_source.source3.cached_param3 #end if
  alignments
#if $cond_source.source4.source4_source=="user" $cond_source.source4.user_param4 #else $cond_source.source4.cached_param4 #end if
  outorder
#if $cond_source.source5.source5_source=="user" $cond_source.source5.user_param5 #else $cond_source.source5.cached_param5 #end if
  sequence
#if $cond_source.source6.source6_source=="user" $cond_source.source6.user_param6 #else $cond_source.source6.cached_param6 #end if
  ktup
#if $cond_source.source7.source7_source=="user" $cond_source.source7.user_param7 #else $cond_source.source7.cached_param7 #end if
  window
#if $cond_source.source8.source8_source=="user" $cond_source.source8.user_param8 #else $cond_source.source8.cached_param8 #end if
  score
#if $cond_source.source9.source9_source=="user" $cond_source.source9.user_param9 #else $cond_source.source9.cached_param9 #end if
  topdiag
#if $cond_source.source10.source10_source=="user" $cond_source.source10.user_param10 #else $cond_source.source10.cached_param10 #end if
  pairgap
#if $cond_source.source11.source11_source=="user" $cond_source.source11.user_param11 #else $cond_source.source11.cached_param11 #end if
  pwmatrix
#if $cond_source.source12.source12_source=="user" $cond_source.source12.user_param12 #else $cond_source.source12.cached_param12 #end if
  pwdnamatrix
#if $cond_source.source13.source13_source=="user" $cond_source.source13.user_param13 #else $cond_source.source13.cached_param13 #end if
  pwgapopen
#if $cond_source.source14.source14_source=="user" $cond_source.source14.user_param14 #else $cond_source.source14.cached_param14 #end if
  pwgapext
#if $cond_source.source15.source15_source=="user" $cond_source.source15.user_param15 #else $cond_source.source15.cached_param15 #end if
  matrix
#if $cond_source.source16.source16_source=="user" $cond_source.source16.user_param16 #else $cond_source.source16.cached_param16 #end if
  dnamatrix
#if $cond_source.source17.source17_source=="user" $cond_source.source17.user_param17 #else $cond_source.source17.cached_param17 #end if
  gapopen
#if $cond_source.source18.source18_source=="user" $cond_source.source18.user_param18 #else $cond_source.source18.cached_param18 #end if
  noendgaps
#if $cond_source.source19.source19_source=="user" $cond_source.source19.user_param19 #else $cond_source.source19.cached_param19 #end if
  gapext
#if $cond_source.source20.source20_source=="user" $cond_source.source20.user_param20 #else $cond_source.source20.cached_param20 #end if
  gapext
#if $cond_source.source21.source21_source=="user" $cond_source.source21.user_param21 #else $cond_source.source21.cached_param21 #end if
  iteration
#if $cond_source.source22.source22_source=="user" $cond_source.source22.user_param22 #else $cond_source.source22.cached_param22 #end if
  numiter
#if $cond_source.source23.source23_source=="user" $cond_source.source23.user_param23 #else $cond_source.source23.cached_param23 #end if
#else 
#end if
</command>
  <inputs>
<conditional name="source0">
    <param name="source0_source" type="select" label="id 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 format="text" size = "150" name = "user_param0"  type="text" label="Enter email" help="see tip below" />
 </when>
 <when value="cached">
    <param name = "cached_param0" type="data" label="Choose the step from which to get the parameter id"/> 
 </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="source1">
  <param name="source1_source" type="select" label="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_param1" type="select" label="Select type" help="see tip below">
 <option value="protein" selected="true">protein</option>
  <option value="dna" >dna</option>
     </param> 
 </when>
<when value="cached">
 <param name = "cached_param1" type="data" label="Choose the step from which to get the parameter type"/> 
  </when></conditional>

<conditional name="source2">
  <param name="source2_source" type="select" label="title 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 format="text" size = "150" name = "user_param2"  type="text" label="Enter title" help="see tip below" />
 </when>
<when value="cached">
 <param name = "cached_param2" type="data" label="Choose the step from which to get the parameter title"/> 
  </when></conditional>

<conditional name="source3">
  <param name="source3_source" type="select" label="output 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" help="see tip below">
 <option value="aln1" selected="true">aln1</option>
  <option value="aln2" >aln2</option>
  <option value="gcg" >gcg</option>
  <option value="phylip" >phylip</option>
  <option value="nexus" >nexus</option>
  <option value="pir" >pir</option>
  <option value="gde" >gde</option>
  <option value="fasta" >fasta</option>
     </param> 
 </when>
<when value="cached">
 <param name = "cached_param3" type="data" label="Choose the step from which to get the parameter output"/> 
  </when></conditional>

<conditional name="source4">
  <param name="source4_source" type="select" label="alignments 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 alignments" help="see tip below">
 <option value="slow" selected="true">slow</option>
  <option value="fast" >fast</option>
     </param> 
 </when>
<when value="cached">
 <param name = "cached_param4" type="data" label="Choose the step from which to get the parameter alignments"/> 
  </when></conditional>

<conditional name="source5">
  <param name="source5_source" type="select" label="outorder 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_param5" type="select" label="Select outorder" help="see tip below">
 <option value="aligned" selected="true">aligned</option>
  <option value="input" >input</option>
     </param> 
 </when>
<when value="cached">
 <param name = "cached_param5" type="data" label="Choose the step from which to get the parameter outorder"/> 
  </when></conditional>

<conditional name="source6">
  <param name="source6_source" type="select" label="sequence 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 format="text" size = "150" name = "user_param6"  type="text" label="Enter sequence" help="see tip below" />
 </when>
<when value="cached">
 <param name = "cached_param6" type="data" label="Choose the step from which to get the parameter sequence"/> 
  </when></conditional>

<conditional name="source7">
  <param name="source7_source" type="select" label="ktup 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_param7" type="select" label="Select ktup" help="see tip below">
 <option value="1" selected="true">1</option>
  <option value="2" >2</option>
  <option value="3" >3</option>
  <option value="4" >4</option>
  <option value="5" >5</option>
     </param> 
 </when>
<when value="cached">
 <param name = "cached_param7" type="data" label="Choose the step from which to get the parameter ktup"/> 
  </when></conditional>

<conditional name="source8">
  <param name="source8_source" type="select" label="window 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_param8" type="select" label="Select window" help="see tip below">
 <option value="10" >10</option>
  <option value="9" >9</option>
  <option value="8" >8</option>
  <option value="7" >7</option>
  <option value="6" >6</option>
  <option value="5" selected="true">5</option>
  <option value="4" >4</option>
  <option value="3" >3</option>
  <option value="2" >2</option>
  <option value="1" >1</option>
  <option value="0" >0</option>
     </param> 
 </when>
<when value="cached">
 <param name = "cached_param8" type="data" label="Choose the step from which to get the parameter window"/> 
  </when></conditional>

<conditional name="source9">
  <param name="source9_source" type="select" label="score 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_param9" type="select" label="Select score" help="see tip below">
 <option value="percent" selected="true">percent</option>
  <option value="absolute" >absolute</option>
     </param> 
 </when>
<when value="cached">
 <param name = "cached_param9" type="data" label="Choose the step from which to get the parameter score"/> 
  </when></conditional>

<conditional name="source10">
  <param name="source10_source" type="select" label="topdiag 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_param10" type="select" label="Select topdiag" help="see tip below">
 <option value="10" >10</option>
  <option value="9" >9</option>
  <option value="8" >8</option>
  <option value="7" >7</option>
  <option value="6" >6</option>
  <option value="5" selected="true">5</option>
  <option value="4" >4</option>
  <option value="3" >3</option>
  <option value="2" >2</option>
  <option value="1" >1</option>
     </param> 
 </when>
<when value="cached">
 <param name = "cached_param10" type="data" label="Choose the step from which to get the parameter topdiag"/> 
  </when></conditional>

<conditional name="source11">
  <param name="source11_source" type="select" label="pairgap 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_param11" type="select" label="Select pairgap" help="see tip below">
 <option value="1" >1</option>
  <option value="2" >2</option>
  <option value="3" selected="true">3</option>
  <option value="4" >4</option>
  <option value="5" >5</option>
  <option value="10" >10</option>
  <option value="25" >25</option>
  <option value="50" >50</option>
  <option value="100" >100</option>
  <option value="250" >250</option>
  <option value="500" >500</option>
     </param> 
 </when>
<when value="cached">
 <param name = "cached_param11" type="data" label="Choose the step from which to get the parameter pairgap"/> 
  </when></conditional>

<conditional name="source12">
  <param name="source12_source" type="select" label="pwmatrix 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_param12" type="select" label="Select pwmatrix" help="see tip below">
 <option value="blosum" >blosum</option>
  <option value="pam" >pam</option>
  <option value="gonnet" selected="true">gonnet</option>
  <option value="id" >id</option>
     </param> 
 </when>
<when value="cached">
 <param name = "cached_param12" type="data" label="Choose the step from which to get the parameter pwmatrix"/> 
  </when></conditional>

<conditional name="source13">
  <param name="source13_source" type="select" label="pwdnamatrix 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_param13" type="select" label="Select pwdnamatrix" help="see tip below">
 <option value="iub" selected="true">iub</option>
  <option value="clustalw" >clustalw</option>
     </param> 
 </when>
<when value="cached">
 <param name = "cached_param13" type="data" label="Choose the step from which to get the parameter pwdnamatrix"/> 
  </when></conditional>

<conditional name="source14">
  <param name="source14_source" type="select" label="pwgapopen 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_param14" type="select" label="Select pwgapopen" help="see tip below">
 <option value="100" >100</option>
  <option value="50" >50</option>
  <option value="25" >25</option>
  <option value="10" selected="true">10</option>
  <option value="5" >5</option>
  <option value="2" >2</option>
  <option value="1" >1</option>
     </param> 
 </when>
<when value="cached">
 <param name = "cached_param14" type="data" label="Choose the step from which to get the parameter pwgapopen"/> 
  </when></conditional>

<conditional name="source15">
  <param name="source15_source" type="select" label="pwgapext 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_param15" type="select" label="Select pwgapext" help="see tip below">
 <option value="0.05" >0.05</option>
  <option value="0.1" selected="true">0.1</option>
  <option value="0.5" >0.5</option>
  <option value="1.0" >1.0</option>
  <option value="2.5" >2.5</option>
  <option value="5.0" >5.0</option>
  <option value="7.5" >7.5</option>
  <option value="10.0" >10.0</option>
     </param> 
 </when>
<when value="cached">
 <param name = "cached_param15" type="data" label="Choose the step from which to get the parameter pwgapext"/> 
  </when></conditional>

<conditional name="source16">
  <param name="source16_source" type="select" label="matrix 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_param16" type="select" label="Select matrix" help="see tip below">
 <option value="blosum" >blosum</option>
  <option value="pam" >pam</option>
  <option value="gonnet" selected="true">gonnet</option>
  <option value="id" >id</option>
     </param> 
 </when>
<when value="cached">
 <param name = "cached_param16" type="data" label="Choose the step from which to get the parameter matrix"/> 
  </when></conditional>

<conditional name="source17">
  <param name="source17_source" type="select" label="dnamatrix 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_param17" type="select" label="Select dnamatrix" help="see tip below">
 <option value="iub" selected="true">iub</option>
  <option value="clustalw" >clustalw</option>
     </param> 
 </when>
<when value="cached">
 <param name = "cached_param17" type="data" label="Choose the step from which to get the parameter dnamatrix"/> 
  </when></conditional>

<conditional name="source18">
  <param name="source18_source" type="select" label="gapopen 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_param18" type="select" label="Select gapopen" help="see tip below">
 <option value="100" >100</option>
  <option value="50" >50</option>
  <option value="25" >25</option>
  <option value="10" selected="true">10</option>
  <option value="5" >5</option>
  <option value="2" >2</option>
  <option value="1" >1</option>
     </param> 
 </when>
<when value="cached">
 <param name = "cached_param18" type="data" label="Choose the step from which to get the parameter gapopen"/> 
  </when></conditional>

<conditional name="source19">
  <param name="source19_source" type="select" label="noendgaps 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_param19" type="select" label="Select noendgaps" help="see tip below">
 <option value="false" selected="true">false</option>
  <option value="true" >true</option>
     </param> 
 </when>
<when value="cached">
 <param name = "cached_param19" type="data" label="Choose the step from which to get the parameter noendgaps"/> 
  </when></conditional>

<conditional name="source20">
  <param name="source20_source" type="select" label="gapext 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_param20" type="select" label="Select gapext" help="see tip below">
 <option value="0.05" >0.05</option>
  <option value="0.20" selected="true">0.20</option>
  <option value="0.5" >0.5</option>
  <option value="1.0" >1.0</option>
  <option value="2.5" >2.5</option>
  <option value="5.0" >5.0</option>
  <option value="7.5" >7.5</option>
  <option value="10.0" >10.0</option>
     </param> 
 </when>
<when value="cached">
 <param name = "cached_param20" type="data" label="Choose the step from which to get the parameter gapext"/> 
  </when></conditional>

<conditional name="source21">
  <param name="source21_source" type="select" label="gapext 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_param21" type="select" label="Select gapext" help="see tip below">
 <option value="10" >10</option>
  <option value="9" >9</option>
  <option value="8" >8</option>
  <option value="7" >7</option>
  <option value="6" >6</option>
  <option value="5" selected="true">5</option>
  <option value="4" >4</option>
  <option value="3" >3</option>
  <option value="2" >2</option>
  <option value="1" >1</option>
     </param> 
 </when>
<when value="cached">
 <param name = "cached_param21" type="data" label="Choose the step from which to get the parameter gapext"/> 
  </when></conditional>

<conditional name="source22">
  <param name="source22_source" type="select" label="iteration 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_param22" type="select" label="Select iteration" help="see tip below">
 <option value="none" >none</option>
  <option value="tree" >tree</option>
  <option value="alignment" >alignment</option>
     </param> 
 </when>
<when value="cached">
 <param name = "cached_param22" type="data" label="Choose the step from which to get the parameter iteration"/> 
  </when></conditional>

<conditional name="source23">
  <param name="source23_source" type="select" label="numiter 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_param23" type="select" label="Select numiter" help="see tip below">
 <option value="1" selected="true">1</option>
  <option value="2" >2</option>
  <option value="3" >3</option>
  <option value="4" >4</option>
  <option value="5" >5</option>
  <option value="6" >6</option>
  <option value="7" >7</option>
  <option value="8" >8</option>
  <option value="9" >9</option>
  <option value="10" >10</option>
     </param> 
 </when>
<when value="cached">
 <param name = "cached_param23" type="data" label="Choose the step from which to get the parameter numiter"/> 
  </when></conditional>
 </when>
 </conditional>
</inputs>
  <outputs>
    <data format="tabular" name="output" />
  </outputs>
  <help>

.. class:: infomark

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