comparison snpindex.xml @ 5:14561eb803a5 draft

Uploaded v3.0.1b (still working on this prior to main Tool Shed release)

4:a88571642c6e

  <description>build index files for known SNPs</description>
  <requirements>
      <requirement type="package" version="2013-05-09">gmap</requirement>
  </requirements>
  <version_command>snpindex --version</version_command>
  <command interpreter="command"> /bin/bash $shscript 2>1 1> $output </command>
  <configfiles>
    <configfile name="shscript">
#!/bin/bash
#set $ds = chr(36)
#set $gt = chr(62)
#set $lt = chr(60)
#set $ad = chr(38)

cat $dbsnp.snps  > $pathsnpsiit
#end if
snpindex -D $gmapdb -d $refname -V $output.extra_files_path -v $snpsname $pathsnpsiit
echo snpindex -D  $gmapdb -d $refname -V $output.extra_files_path -v $snpsname $pathsnpsiit
#end if
    </configfile>
  </configfiles>
  <inputs>
    <conditional name="refGenomeSource">
     <param name="genomeSource" type="select" label="Will you map to a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
        <option value="indexed">Use a built-in index</option>
        <option value="gmapdb">Use gmapdb from the history</option>
      </param>
      <when value="indexed">
        <param name="gmapindex" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
          <options from_file="gmap_indices.loc">
            <column name="uid" index="0" />
            <column name="dbkey" index="1" />
            <column name="name" index="2" />
            <column name="kmers" index="3" />
            <column name="maps" index="4" />

5:14561eb803a5

  <description>build index files for known SNPs</description>
  <requirements>
      <requirement type="package" version="2013-05-09">gmap</requirement>
  </requirements>
  <version_command>snpindex --version</version_command>
  <command detect_errors="exit_code" interpreter="bash"><![CDATA[
$shscript 2>1 1> $output
  ]]></command>
  <configfiles>
    <configfile name="shscript"><![CDATA[
#!/bin/bash
#set $ds = chr(36)
#set $gt = chr(62)
#set $lt = chr(60)
#set $ad = chr(38)

cat $dbsnp.snps  > $pathsnpsiit
#end if
snpindex -D $gmapdb -d $refname -V $output.extra_files_path -v $snpsname $pathsnpsiit
echo snpindex -D  $gmapdb -d $refname -V $output.extra_files_path -v $snpsname $pathsnpsiit
#end if
    ]]></configfile>
  </configfiles>
  <inputs>
    <conditional name="refGenomeSource">
     <param name="genomeSource" type="select" label="Will you map to a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
        <option value="indexed">Use a built-in index</option>
        <option value="gmapdb">Use gmapdb from the history</option>
      </param>
      <when value="indexed">
        <param name="gmapindex" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
          <options from_data_table="gmap_indices">
            <column name="uid" index="0" />
            <column name="dbkey" index="1" />
            <column name="name" index="2" />
            <column name="kmers" index="3" />
            <column name="maps" index="4" />